2021-08-29 04:05:26,671 INFO BenchmarkPipeline --- START PROCESSING 'SRR3733922' --- 2021-08-29 04:05:26,671 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3733922.sra 2021-08-29 04:05:26,671 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__ 2021-08-29 04:05:26,671 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmphjpqdzfe "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR3733922.sra" 2021-08-29 04:23:28,305 INFO SimpleSubprocess Sra2FastQ - 0:18:01 2021-08-29 04:23:28,332 DEBUG SimpleSubprocess gzip /tmp/tmphjpqdzfe/* 2021-08-29 05:11:10,511 INFO SimpleSubprocess GZipFastQ - 0:47:42 2021-08-29 05:11:10,512 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/fastq"; mv /tmp/tmphjpqdzfe/SRR3733922_1.fastq.gz /tmp/tmphjpqdzfe/SRR3733922_R1.fastq.gz; mv /tmp/tmphjpqdzfe/SRR3733922_2.fastq.gz /tmp/tmphjpqdzfe/SRR3733922_R2.fastq.gz; cp /tmp/tmphjpqdzfe/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/fastq" 2021-08-29 05:11:31,563 INFO SimpleSubprocess CopyFiles - 0:00:21 2021-08-29 05:11:33,055 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__ 2021-08-29 05:11:33,055 INFO Juicer Genome assembly: mm10 2021-08-29 05:11:33,055 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-29 05:11:33,055 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 05:11:33,055 INFO Juicer Enzyme: DpnII 2021-08-29 05:11:33,055 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-29 05:11:33,055 INFO Juicer Threads: 10 2021-08-29 05:11:33,056 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/SRR3733922/__temp__" 2021-08-29 09:56:47,860 INFO SimpleSubprocess Juicer - 4:45:14 2021-08-29 09:56:47,975 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/SRR3733922/__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/SRR3733922/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/splits/SRR3733922_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/splits/SRR3733922_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/splits/SRR3733922.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/splits/SRR3733922.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 [2021-08-29T09:01:12,616] [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 [2021-08-29T09:34:18,345] [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/SRR3733922/__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 [2021-08-29T09:56:47,278] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__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/SRR3733922/__temp__/aligned for results 2021-08-29 09:56:48,057 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/merged_nodups.txt 2021-08-29 09:56:48,057 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter.pairs.txt 2021-08-29 09:56:48,058 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp5n7m3dvc/inter.pairs.txt" 2021-08-29 09:57:38,544 INFO SimpleSubprocess MakeInterPairs - 0:00:50 2021-08-29 09:57:38,544 DEBUG SimpleSubprocess cp "/tmp/tmp5n7m3dvc/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter.pairs.txt" 2021-08-29 09:57:39,920 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-08-29 09:57:40,214 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter.pairs.txt 2021-08-29 09:57:40,214 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-29 09:57:40,215 INFO Pairs2Cool Genome assembly: mm10 2021-08-29 09:57:40,215 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 09:57:40,215 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-29 09:57:40,239 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/SRR3733922/__temp__/aligned/inter.pairs.txt" "/tmp/tmp2t3uj2ab/inter_no_balanced.cool" 2021-08-29 09:59:05,491 INFO SimpleSubprocess MakeCool - 0:01:25 2021-08-29 09:59:05,491 DEBUG SimpleSubprocess cp "/tmp/tmp2t3uj2ab/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-29 09:59:05,542 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 09:59:05,546 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter.pairs.txt 2021-08-29 09:59:05,546 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-29 09:59:05,546 INFO Pairs2Cool Genome assembly: mm10 2021-08-29 09:59:05,546 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 09:59:05,546 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-29 09:59:05,566 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/SRR3733922/__temp__/aligned/inter.pairs.txt" "/tmp/tmpo29mkxzx/inter_no_balanced.cool" 2021-08-29 10:00:21,252 INFO SimpleSubprocess MakeCool - 0:01:15 2021-08-29 10:00:21,252 DEBUG SimpleSubprocess cp "/tmp/tmpo29mkxzx/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-29 10:00:21,279 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 10:00:21,282 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter.pairs.txt 2021-08-29 10:00:21,282 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-29 10:00:21,283 INFO Pairs2Cool Genome assembly: mm10 2021-08-29 10:00:21,283 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 10:00:21,283 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-29 10:00:21,296 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/SRR3733922/__temp__/aligned/inter.pairs.txt" "/tmp/tmpyi7xztum/inter_no_balanced.cool" 2021-08-29 10:01:33,516 INFO SimpleSubprocess MakeCool - 0:01:12 2021-08-29 10:01:33,517 DEBUG SimpleSubprocess cp "/tmp/tmpyi7xztum/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-29 10:01:33,540 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 10:01:33,575 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter.pairs.txt 2021-08-29 10:01:33,576 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-29 10:01:33,576 INFO Pairs2Cool Genome assembly: mm10 2021-08-29 10:01:33,576 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 10:01:33,576 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-29 10:01:33,576 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/SRR3733922/__temp__/aligned/inter.pairs.txt" "/tmp/tmpfpikfqqn/inter_no_balanced.cool" 2021-08-29 10:02:42,795 INFO SimpleSubprocess MakeCool - 0:01:09 2021-08-29 10:02:42,795 DEBUG SimpleSubprocess cp "/tmp/tmpfpikfqqn/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-29 10:02:42,815 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 10:02:42,818 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter.pairs.txt 2021-08-29 10:02:42,818 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-29 10:02:42,818 INFO Pairs2Cool Genome assembly: mm10 2021-08-29 10:02:42,818 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-29 10:02:42,818 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-29 10:02:42,819 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/SRR3733922/__temp__/aligned/inter.pairs.txt" "/tmp/tmpzdldog1r/inter_no_balanced.cool" 2021-08-29 10:03:50,119 INFO SimpleSubprocess MakeCool - 0:01:07 2021-08-29 10:03:50,119 DEBUG SimpleSubprocess cp "/tmp/tmpzdldog1r/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-29 10:03:50,137 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 10:03:50,141 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-29 10:03:50,141 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_5kb.cool 2021-08-29 10:03:50,141 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-29 10:03:50,184 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpzi_yd8fx/inter.cool" 2021-08-29 10:03:50,213 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 10:03:50,214 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpzi_yd8fx/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-29 10:03:55,643 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-08-29 10:03:55,643 DEBUG SimpleSubprocess cp "/tmp/tmpzi_yd8fx/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_5kb.cool" 2021-08-29 10:03:55,672 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 10:03:55,676 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-29 10:03:55,676 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_10kb.cool 2021-08-29 10:03:55,676 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-29 10:03:55,693 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpxoqsr3h5/inter.cool" 2021-08-29 10:03:55,718 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 10:03:55,718 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpxoqsr3h5/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-29 10:03:58,290 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-29 10:03:58,291 DEBUG SimpleSubprocess cp "/tmp/tmpxoqsr3h5/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_10kb.cool" 2021-08-29 10:03:58,315 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 10:03:58,318 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-29 10:03:58,319 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_20kb.cool 2021-08-29 10:03:58,319 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-29 10:03:58,319 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp4xkv4qcc/inter.cool" 2021-08-29 10:03:58,341 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 10:03:58,341 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp4xkv4qcc/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-29 10:04:00,204 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-29 10:04:00,204 DEBUG SimpleSubprocess cp "/tmp/tmp4xkv4qcc/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_20kb.cool" 2021-08-29 10:04:00,226 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 10:04:00,229 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-29 10:04:00,229 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_25kb.cool 2021-08-29 10:04:00,229 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-29 10:04:00,365 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpce7rsgqg/inter.cool" 2021-08-29 10:04:00,386 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 10:04:00,387 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpce7rsgqg/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-29 10:04:02,070 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-29 10:04:02,071 DEBUG SimpleSubprocess cp "/tmp/tmpce7rsgqg/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_25kb.cool" 2021-08-29 10:04:02,092 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 10:04:02,094 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-29 10:04:02,094 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_50kb.cool 2021-08-29 10:04:02,094 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-08-29 10:04:02,095 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpad1efelk/inter.cool" 2021-08-29 10:04:02,112 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 10:04:02,113 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpad1efelk/inter.cool" "chr11:109,140,001-115,015,000" 2021-08-29 10:04:03,366 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-29 10:04:03,367 DEBUG SimpleSubprocess cp "/tmp/tmpad1efelk/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_50kb.cool" 2021-08-29 10:04:03,385 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 10:04:03,430 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/vector.txt 2021-08-29 10:04:03,436 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-29 10:04:03,436 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_5kb.cool 2021-08-29 10:04:03,436 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/vector.txt 2021-08-29 10:04:03,436 INFO AddWeight Chromosome: chr11 2021-08-29 10:04:03,436 INFO AddWeight Resolution [bp]: 5000 2021-08-29 10:04:03,561 INFO AddWeight AddWeight successfully finished 2021-08-29 10:04:03,561 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_10kb.cool 2021-08-29 10:04:03,561 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/vector.txt 2021-08-29 10:04:03,561 INFO AddWeight Chromosome: chr11 2021-08-29 10:04:03,562 INFO AddWeight Resolution [bp]: 10000 2021-08-29 10:04:03,610 INFO AddWeight AddWeight successfully finished 2021-08-29 10:04:03,610 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_20kb.cool 2021-08-29 10:04:03,610 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/vector.txt 2021-08-29 10:04:03,610 INFO AddWeight Chromosome: chr11 2021-08-29 10:04:03,610 INFO AddWeight Resolution [bp]: 20000 2021-08-29 10:04:03,641 INFO AddWeight AddWeight successfully finished 2021-08-29 10:04:03,641 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_25kb.cool 2021-08-29 10:04:03,642 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/vector.txt 2021-08-29 10:04:03,642 INFO AddWeight Chromosome: chr11 2021-08-29 10:04:03,642 INFO AddWeight Resolution [bp]: 25000 2021-08-29 10:04:03,669 INFO AddWeight AddWeight successfully finished 2021-08-29 10:04:03,669 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_50kb.cool 2021-08-29 10:04:03,669 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/vector.txt 2021-08-29 10:04:03,669 INFO AddWeight Chromosome: chr11 2021-08-29 10:04:03,669 INFO AddWeight Resolution [bp]: 50000 2021-08-29 10:04:03,689 INFO AddWeight AddWeight successfully finished 2021-08-29 10:04:03,691 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter.hic 2021-08-29 10:04:03,691 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_norm.hic 2021-08-29 10:04:03,691 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/vector.txt 2021-08-29 10:04:03,691 INFO Vector2HiC Threads: 10 2021-08-29 10:04:03,769 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter.hic" "/tmp/tmposfpzr1n/inter.hic" 2021-08-29 10:04:04,024 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-29 10:04:04,025 INFO Vector2HiC Vector: vector c-tale_normalization chr11 5000 BP 2021-08-29 10:04:04,026 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmposfpzr1n/inter.hic" "/tmp/tmposfpzr1n/vector.txt" 2021-08-29 10:04:08,585 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-29 10:04:08,586 INFO Vector2HiC Vector: vector c-tale_normalization chr11 10000 BP 2021-08-29 10:04:08,587 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmposfpzr1n/inter.hic" "/tmp/tmposfpzr1n/vector.txt" 2021-08-29 10:04:12,452 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-29 10:04:12,452 INFO Vector2HiC Vector: vector c-tale_normalization chr11 20000 BP 2021-08-29 10:04:12,453 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmposfpzr1n/inter.hic" "/tmp/tmposfpzr1n/vector.txt" 2021-08-29 10:04:16,096 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-29 10:04:16,097 INFO Vector2HiC Vector: vector c-tale_normalization chr11 25000 BP 2021-08-29 10:04:16,097 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmposfpzr1n/inter.hic" "/tmp/tmposfpzr1n/vector.txt" 2021-08-29 10:04:19,788 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-29 10:04:19,788 INFO Vector2HiC Vector: vector c-tale_normalization chr11 50000 BP 2021-08-29 10:04:19,788 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmposfpzr1n/inter.hic" "/tmp/tmposfpzr1n/vector.txt" 2021-08-29 10:04:23,498 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-29 10:04:23,498 DEBUG SimpleSubprocess cp "/tmp/tmposfpzr1n/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_norm.hic" 2021-08-29 10:04:23,824 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-29 10:04:23,876 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/merged_nodups.txt" 2021-08-29 10:04:46,392 INFO SimpleSubprocess CopyResult - 0:00:22 2021-08-29 10:04:46,392 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter.pairs.txt" 2021-08-29 10:04:58,511 INFO SimpleSubprocess CopyResult - 0:00:12 2021-08-29 10:04:58,511 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/vector.txt" 2021-08-29 10:04:58,519 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:04:58,520 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter.hic" 2021-08-29 10:05:01,243 INFO SimpleSubprocess CopyResult - 0:00:02 2021-08-29 10:05:01,243 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter_statistics.txt" 2021-08-29 10:05:01,251 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:05:01,251 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter_no_balanced_5kb.cool" 2021-08-29 10:05:01,387 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:05:01,388 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter_5kb.cool" 2021-08-29 10:05:01,552 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:05:01,552 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter_no_balanced_10kb.cool" 2021-08-29 10:05:01,712 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:05:01,712 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter_10kb.cool" 2021-08-29 10:05:01,876 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:05:01,876 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter_no_balanced_20kb.cool" 2021-08-29 10:05:02,023 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:05:02,023 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter_20kb.cool" 2021-08-29 10:05:02,151 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:05:02,151 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter_no_balanced_25kb.cool" 2021-08-29 10:05:02,283 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:05:02,284 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter_25kb.cool" 2021-08-29 10:05:02,415 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:05:02,415 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter_no_balanced_50kb.cool" 2021-08-29 10:05:02,516 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:05:02,516 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/inter_50kb.cool" 2021-08-29 10:05:02,615 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-29 10:05:02,919 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__" 2021-08-29 10:05:12,002 INFO SimpleSubprocess RemoveTemp - 0:00:09 2021-08-29 10:05:12,002 INFO BenchmarkPipeline 'SRR3733922' FINISHED, SUMMARY TIME - 5:59:45 2021-09-01 12:23:13,356 INFO BenchmarkPipeline --- START PROCESSING 'SRR3733922' --- 2021-09-01 12:23:13,357 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__" 2021-09-01 12:23:13,366 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-01 12:23:13,366 INFO BenchmarkPipeline 'SRR3733922' FINISHED, SUMMARY TIME - 0:00:00 2021-09-02 13:38:17,810 INFO BenchmarkPipeline --- START PROCESSING 'SRR3733922' --- 2021-09-02 13:38:17,810 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR3733922/__temp__" 2021-09-02 13:38:17,817 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-02 13:38:17,818 INFO BenchmarkPipeline 'SRR3733922' FINISHED, SUMMARY TIME - 0:00:00