2021-08-29 15:14:17,188 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099905' --- 2021-08-29 15:14:17,188 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099905.sra 2021-08-29 15:14:17,188 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__ 2021-08-29 15:14:17,189 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp148ht8b7 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5099905.sra" 2021-08-29 15:30:42,974 INFO SimpleSubprocess Sra2FastQ - 0:16:25 2021-08-29 15:30:42,974 DEBUG SimpleSubprocess gzip /tmp/tmp148ht8b7/* 2021-08-29 16:04:49,929 INFO SimpleSubprocess GZipFastQ - 0:34:06 2021-08-29 16:04:49,970 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/fastq"; mv /tmp/tmp148ht8b7/SRR5099905_2.fastq.gz /tmp/tmp148ht8b7/SRR5099905_R2.fastq.gz; mv /tmp/tmp148ht8b7/SRR5099905_1.fastq.gz /tmp/tmp148ht8b7/SRR5099905_R1.fastq.gz; cp /tmp/tmp148ht8b7/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/fastq" 2021-08-29 16:04:56,343 INFO SimpleSubprocess CopyFiles - 0:00:06 2021-08-29 16:04:57,274 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__ 2021-08-29 16:04:57,274 INFO Juicer Genome assembly: hg38 2021-08-29 16:04:57,274 INFO Juicer Genome FASTA path: /Data/DataBases/hg38/hg38_canonic.fa 2021-08-29 16:04:57,274 INFO Juicer Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 16:04:57,274 INFO Juicer Enzyme: DpnII 2021-08-29 16:04:57,274 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_hg38.txt 2021-08-29 16:04:57,274 INFO Juicer Threads: 10 2021-08-29 16:04:57,275 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 hg38 -z "/Data/DataBases/hg38/hg38_canonic.fa" -p "/Data/DataBases/hg38/hg38_canonic.chrom.sizes" -s DpnII -y "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_hg38.txt" -d "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__" 2021-08-29 19:41:39,753 INFO SimpleSubprocess Juicer - 3:36:42 2021-08-29 19:41:39,849 INFO Juicer Using /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_hg38.txt as site file (-: Looking for fastq files...fastq files exist (-: Aligning files matching /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/fastq/*_R*.fastq* to genome hg38 with site file /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_hg38.txt (-: Created /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/hg38/hg38_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/splits/SRR5099905_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/splits/SRR5099905_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/splits/SRR5099905.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/splits/SRR5099905.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 [2021-08-29T19:04:36,154] [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 [2021-08-29T19:26:36,526] [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 hg38 Data read from /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__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 [2021-08-29T19:41:39,153] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__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/SRR5099905/__temp__/aligned for results 2021-08-29 19:41:39,941 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/merged_nodups.txt 2021-08-29 19:41:39,941 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt 2021-08-29 19:41:39,942 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpw5uvnoue/inter.pairs.txt" 2021-08-29 19:42:10,405 INFO SimpleSubprocess MakeInterPairs - 0:00:30 2021-08-29 19:42:10,405 DEBUG SimpleSubprocess cp "/tmp/tmpw5uvnoue/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt" 2021-08-29 19:42:11,262 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:42:11,423 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt 2021-08-29 19:42:11,423 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-29 19:42:11,423 INFO Pairs2Cool Genome assembly: hg38 2021-08-29 19:42:11,423 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 19:42:11,423 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-29 19:42:11,449 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly hg38 "/Data/DataBases/hg38/hg38_canonic.chrom.sizes":5000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt" "/tmp/tmpf006vlts/inter_no_balanced.cool" 2021-08-29 19:43:09,024 INFO SimpleSubprocess MakeCool - 0:00:57 2021-08-29 19:43:09,024 DEBUG SimpleSubprocess cp "/tmp/tmpf006vlts/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-29 19:43:09,076 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:43:09,079 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt 2021-08-29 19:43:09,079 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-29 19:43:09,079 INFO Pairs2Cool Genome assembly: hg38 2021-08-29 19:43:09,079 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 19:43:09,079 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-29 19:43:09,079 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly hg38 "/Data/DataBases/hg38/hg38_canonic.chrom.sizes":10000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt" "/tmp/tmp4qwvfopw/inter_no_balanced.cool" 2021-08-29 19:43:54,959 INFO SimpleSubprocess MakeCool - 0:00:45 2021-08-29 19:43:54,959 DEBUG SimpleSubprocess cp "/tmp/tmp4qwvfopw/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-29 19:43:54,979 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:43:55,000 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt 2021-08-29 19:43:55,000 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-29 19:43:55,000 INFO Pairs2Cool Genome assembly: hg38 2021-08-29 19:43:55,000 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 19:43:55,000 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-29 19:43:55,039 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly hg38 "/Data/DataBases/hg38/hg38_canonic.chrom.sizes":20000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt" "/tmp/tmpj3xwte9r/inter_no_balanced.cool" 2021-08-29 19:44:38,613 INFO SimpleSubprocess MakeCool - 0:00:43 2021-08-29 19:44:38,614 DEBUG SimpleSubprocess cp "/tmp/tmpj3xwte9r/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-29 19:44:38,630 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:44:38,652 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt 2021-08-29 19:44:38,652 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-29 19:44:38,652 INFO Pairs2Cool Genome assembly: hg38 2021-08-29 19:44:38,652 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 19:44:38,652 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-29 19:44:38,659 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly hg38 "/Data/DataBases/hg38/hg38_canonic.chrom.sizes":25000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt" "/tmp/tmpm2465ahr/inter_no_balanced.cool" 2021-08-29 19:45:21,372 INFO SimpleSubprocess MakeCool - 0:00:42 2021-08-29 19:45:21,372 DEBUG SimpleSubprocess cp "/tmp/tmpm2465ahr/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-29 19:45:21,388 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:45:21,390 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt 2021-08-29 19:45:21,390 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-29 19:45:21,390 INFO Pairs2Cool Genome assembly: hg38 2021-08-29 19:45:21,390 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/hg38/hg38_canonic.chrom.sizes 2021-08-29 19:45:21,390 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-29 19:45:21,390 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly hg38 "/Data/DataBases/hg38/hg38_canonic.chrom.sizes":50000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt" "/tmp/tmp5kezmeu9/inter_no_balanced.cool" 2021-08-29 19:46:02,422 INFO SimpleSubprocess MakeCool - 0:00:41 2021-08-29 19:46:02,422 DEBUG SimpleSubprocess cp "/tmp/tmp5kezmeu9/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-29 19:46:02,437 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:46:02,440 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-29 19:46:02,440 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_5kb.cool 2021-08-29 19:46:02,440 INFO CTaleNormalize Capture: chr2:217,445,000-223,235,000 2021-08-29 19:46:02,447 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpk1z8w9ue/inter.cool" 2021-08-29 19:46:02,470 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 19:46:02,470 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpk1z8w9ue/inter.cool" "chr2:217,445,000-223,235,000" 2021-08-29 19:46:09,155 INFO SimpleSubprocess NormalizeCool - 0:00:06 2021-08-29 19:46:09,156 DEBUG SimpleSubprocess cp "/tmp/tmpk1z8w9ue/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_5kb.cool" 2021-08-29 19:46:09,179 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:46:09,182 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-29 19:46:09,182 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_10kb.cool 2021-08-29 19:46:09,182 INFO CTaleNormalize Capture: chr2:217,445,000-223,235,000 2021-08-29 19:46:09,214 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpko1iu94l/inter.cool" 2021-08-29 19:46:09,234 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 19:46:09,234 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpko1iu94l/inter.cool" "chr2:217,445,000-223,235,000" 2021-08-29 19:46:12,605 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-08-29 19:46:12,606 DEBUG SimpleSubprocess cp "/tmp/tmpko1iu94l/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_10kb.cool" 2021-08-29 19:46:12,624 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:46:12,626 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-29 19:46:12,627 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_20kb.cool 2021-08-29 19:46:12,627 INFO CTaleNormalize Capture: chr2:217,445,000-223,235,000 2021-08-29 19:46:12,676 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpox8jksyj/inter.cool" 2021-08-29 19:46:12,692 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 19:46:12,692 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpox8jksyj/inter.cool" "chr2:217,445,000-223,235,000" 2021-08-29 19:46:14,884 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-29 19:46:14,884 DEBUG SimpleSubprocess cp "/tmp/tmpox8jksyj/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_20kb.cool" 2021-08-29 19:46:14,925 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:46:14,926 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-29 19:46:14,927 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_25kb.cool 2021-08-29 19:46:14,927 INFO CTaleNormalize Capture: chr2:217,445,000-223,235,000 2021-08-29 19:46:14,938 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpsdlamzhv/inter.cool" 2021-08-29 19:46:14,953 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 19:46:14,953 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpsdlamzhv/inter.cool" "chr2:217,445,000-223,235,000" 2021-08-29 19:46:16,904 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-29 19:46:16,905 DEBUG SimpleSubprocess cp "/tmp/tmpsdlamzhv/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_25kb.cool" 2021-08-29 19:46:16,922 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:46:16,923 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-29 19:46:16,923 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_50kb.cool 2021-08-29 19:46:16,924 INFO CTaleNormalize Capture: chr2:217,445,000-223,235,000 2021-08-29 19:46:16,934 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp3kdp978w/inter.cool" 2021-08-29 19:46:16,948 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 19:46:16,948 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp3kdp978w/inter.cool" "chr2:217,445,000-223,235,000" 2021-08-29 19:46:18,411 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-29 19:46:18,411 DEBUG SimpleSubprocess cp "/tmp/tmp3kdp978w/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_50kb.cool" 2021-08-29 19:46:18,425 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:46:18,428 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/vector.txt 2021-08-29 19:46:18,434 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-29 19:46:18,435 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_5kb.cool 2021-08-29 19:46:18,435 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/vector.txt 2021-08-29 19:46:18,435 INFO AddWeight Chromosome: chr2 2021-08-29 19:46:18,435 INFO AddWeight Resolution [bp]: 5000 2021-08-29 19:46:19,125 INFO AddWeight AddWeight successfully finished 2021-08-29 19:46:19,125 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_10kb.cool 2021-08-29 19:46:19,125 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/vector.txt 2021-08-29 19:46:19,125 INFO AddWeight Chromosome: chr2 2021-08-29 19:46:19,126 INFO AddWeight Resolution [bp]: 10000 2021-08-29 19:46:19,205 INFO AddWeight AddWeight successfully finished 2021-08-29 19:46:19,205 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_20kb.cool 2021-08-29 19:46:19,205 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/vector.txt 2021-08-29 19:46:19,205 INFO AddWeight Chromosome: chr2 2021-08-29 19:46:19,205 INFO AddWeight Resolution [bp]: 20000 2021-08-29 19:46:19,253 INFO AddWeight AddWeight successfully finished 2021-08-29 19:46:19,253 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_25kb.cool 2021-08-29 19:46:19,253 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/vector.txt 2021-08-29 19:46:19,253 INFO AddWeight Chromosome: chr2 2021-08-29 19:46:19,253 INFO AddWeight Resolution [bp]: 25000 2021-08-29 19:46:19,294 INFO AddWeight AddWeight successfully finished 2021-08-29 19:46:19,294 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_50kb.cool 2021-08-29 19:46:19,294 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/vector.txt 2021-08-29 19:46:19,294 INFO AddWeight Chromosome: chr2 2021-08-29 19:46:19,294 INFO AddWeight Resolution [bp]: 50000 2021-08-29 19:46:19,322 INFO AddWeight AddWeight successfully finished 2021-08-29 19:46:19,324 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.hic 2021-08-29 19:46:19,324 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_norm.hic 2021-08-29 19:46:19,324 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/vector.txt 2021-08-29 19:46:19,324 INFO Vector2HiC Threads: 10 2021-08-29 19:46:19,365 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.hic" "/tmp/tmpczg7ftnk/inter.hic" 2021-08-29 19:46:19,608 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 19:46:19,608 INFO Vector2HiC Vector: vector c-tale_normalization chr2 5000 BP 2021-08-29 19:46:19,611 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpczg7ftnk/inter.hic" "/tmp/tmpczg7ftnk/vector.txt" 2021-08-29 19:46:24,298 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-29 19:46:24,299 INFO Vector2HiC Vector: vector c-tale_normalization chr2 10000 BP 2021-08-29 19:46:24,300 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpczg7ftnk/inter.hic" "/tmp/tmpczg7ftnk/vector.txt" 2021-08-29 19:46:28,511 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-29 19:46:28,511 INFO Vector2HiC Vector: vector c-tale_normalization chr2 20000 BP 2021-08-29 19:46:28,512 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpczg7ftnk/inter.hic" "/tmp/tmpczg7ftnk/vector.txt" 2021-08-29 19:46:32,228 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-29 19:46:32,228 INFO Vector2HiC Vector: vector c-tale_normalization chr2 25000 BP 2021-08-29 19:46:32,229 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpczg7ftnk/inter.hic" "/tmp/tmpczg7ftnk/vector.txt" 2021-08-29 19:46:36,244 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-29 19:46:36,244 INFO Vector2HiC Vector: vector c-tale_normalization chr2 50000 BP 2021-08-29 19:46:36,245 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpczg7ftnk/inter.hic" "/tmp/tmpczg7ftnk/vector.txt" 2021-08-29 19:46:40,218 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-29 19:46:40,218 DEBUG SimpleSubprocess cp "/tmp/tmpczg7ftnk/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_norm.hic" 2021-08-29 19:46:40,535 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 19:46:40,615 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/merged_nodups.txt" 2021-08-29 19:46:46,667 INFO SimpleSubprocess CopyResult - 0:00:06 2021-08-29 19:46:46,667 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter.pairs.txt" 2021-08-29 19:46:47,503 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:47,503 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/vector.txt" 2021-08-29 19:46:47,512 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:47,513 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter.hic" 2021-08-29 19:46:47,912 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:47,912 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter_statistics.txt" 2021-08-29 19:46:47,919 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:47,920 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter_no_balanced_5kb.cool" 2021-08-29 19:46:47,949 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:47,950 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter_5kb.cool" 2021-08-29 19:46:47,980 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:47,981 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter_no_balanced_10kb.cool" 2021-08-29 19:46:48,000 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:48,000 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter_10kb.cool" 2021-08-29 19:46:48,028 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:48,028 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter_no_balanced_20kb.cool" 2021-08-29 19:46:48,055 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:48,055 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter_20kb.cool" 2021-08-29 19:46:48,071 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:48,071 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter_no_balanced_25kb.cool" 2021-08-29 19:46:48,087 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:48,087 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter_25kb.cool" 2021-08-29 19:46:48,103 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:48,103 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter_no_balanced_50kb.cool" 2021-08-29 19:46:48,117 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:48,117 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/inter_50kb.cool" 2021-08-29 19:46:48,132 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 19:46:48,349 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__" 2021-08-29 19:46:56,866 INFO SimpleSubprocess RemoveTemp - 0:00:08 2021-08-29 19:46:56,867 INFO BenchmarkPipeline 'SRR5099905' FINISHED, SUMMARY TIME - 4:32:39 2021-09-01 12:23:13,377 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099905' --- 2021-09-01 12:23:13,405 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__" 2021-09-01 12:23:13,415 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,415 INFO BenchmarkPipeline 'SRR5099905' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,827 INFO BenchmarkPipeline --- START PROCESSING 'SRR5099905' --- 2021-09-02 13:38:17,827 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5099905/__temp__" 2021-09-02 13:38:17,835 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,835 INFO BenchmarkPipeline 'SRR5099905' FINISHED, SUMMARY TIME - 0:00:00