2021-09-27 01:21:31,247 INFO BenchmarkPipeline --- START PROCESSING 'SRR8284503-SRR8284504' --- 2021-09-27 01:21:31,247 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284503.sra 2021-09-27 01:21:31,247 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__ 2021-09-27 01:21:31,258 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmprjh5yy9g "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284503.sra" 2021-09-27 01:50:44,733 INFO SimpleSubprocess Sra2FastQ - 0:29:13 2021-09-27 01:50:44,788 DEBUG SimpleSubprocess gzip /tmp/tmprjh5yy9g/* 2021-09-27 03:03:01,925 INFO SimpleSubprocess GZipFastQ - 1:12:17 2021-09-27 03:03:02,148 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/fastq"; mv /tmp/tmprjh5yy9g/SRR8284503_2.fastq.gz /tmp/tmprjh5yy9g/SRR8284503_R2.fastq.gz; mv /tmp/tmprjh5yy9g/SRR8284503_1.fastq.gz /tmp/tmprjh5yy9g/SRR8284503_R1.fastq.gz; cp /tmp/tmprjh5yy9g/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/fastq" 2021-09-27 03:03:54,742 INFO SimpleSubprocess CopyFiles - 0:00:52 2021-09-27 03:03:56,094 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284504.sra 2021-09-27 03:03:56,094 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__ 2021-09-27 03:03:56,095 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpvj6bfv4i "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284504.sra" 2021-09-27 03:31:48,743 INFO SimpleSubprocess Sra2FastQ - 0:27:52 2021-09-27 03:31:48,774 DEBUG SimpleSubprocess gzip /tmp/tmpvj6bfv4i/* 2021-09-27 04:37:26,774 INFO SimpleSubprocess GZipFastQ - 1:05:37 2021-09-27 04:37:26,806 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/fastq"; mv /tmp/tmpvj6bfv4i/SRR8284504_2.fastq.gz /tmp/tmpvj6bfv4i/SRR8284504_R2.fastq.gz; mv /tmp/tmpvj6bfv4i/SRR8284504_1.fastq.gz /tmp/tmpvj6bfv4i/SRR8284504_R1.fastq.gz; cp /tmp/tmpvj6bfv4i/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/fastq" 2021-09-27 04:38:15,943 INFO SimpleSubprocess CopyFiles - 0:00:49 2021-09-27 04:38:17,269 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__ 2021-09-27 04:38:17,311 INFO Juicer Genome assembly: mm10 2021-09-27 04:38:17,311 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-27 04:38:17,311 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-27 04:38:17,311 INFO Juicer Enzyme: DpnII 2021-09-27 04:38:17,311 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-27 04:38:17,311 INFO Juicer Threads: 10 2021-09-27 04:38:17,311 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/HIC_tmp" 2021-09-27 04:38:17,365 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-27 04:38:17,365 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/SRR8284503-SRR8284504/__temp__" 2021-09-28 02:14:18,428 INFO SimpleSubprocess Juicer - 21:36:01 2021-09-28 02:14:18,444 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/SRR8284503-SRR8284504/__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/SRR8284503-SRR8284504/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/splits/SRR8284503_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/splits/SRR8284503_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/splits/SRR8284503.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/splits/SRR8284503.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/splits/SRR8284504_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/splits/SRR8284504_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/splits/SRR8284504.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/splits/SRR8284504.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 [2021-09-28T00:09:48,164] [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 [2021-09-28T01:21:40,595] [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/SRR8284503-SRR8284504/__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 [2021-09-28T02:14:17,972] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__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/SRR8284503-SRR8284504/__temp__/aligned for results 2021-09-28 02:14:18,472 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/merged_nodups.txt 2021-09-28 02:14:18,472 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt 2021-09-28 02:14:18,472 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp0ydygt1a/inter.pairs.txt" 2021-09-28 02:17:17,640 INFO SimpleSubprocess MakeInterPairs - 0:02:59 2021-09-28 02:17:17,640 DEBUG SimpleSubprocess cp "/tmp/tmp0ydygt1a/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt" 2021-09-28 02:17:22,640 INFO SimpleSubprocess CopyFiles - 0:00:05 2021-09-28 02:17:24,074 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt 2021-09-28 02:17:24,075 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-28 02:17:24,075 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 02:17:24,075 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 02:17:24,075 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-28 02:17:24,075 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/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt" "/tmp/tmpoa9xx63v/inter_no_balanced.cool" 2021-09-28 02:22:15,505 INFO SimpleSubprocess MakeCool - 0:04:51 2021-09-28 02:22:15,505 DEBUG SimpleSubprocess cp "/tmp/tmpoa9xx63v/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-28 02:22:15,640 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 02:22:15,653 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt 2021-09-28 02:22:15,654 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-28 02:22:15,654 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 02:22:15,654 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 02:22:15,654 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-28 02:22:15,654 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/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt" "/tmp/tmp6e9ju2ol/inter_no_balanced.cool" 2021-09-28 02:26:48,389 INFO SimpleSubprocess MakeCool - 0:04:32 2021-09-28 02:26:48,390 DEBUG SimpleSubprocess cp "/tmp/tmp6e9ju2ol/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-28 02:26:48,474 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 02:26:48,485 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt 2021-09-28 02:26:48,486 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-28 02:26:48,486 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 02:26:48,486 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 02:26:48,486 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-28 02:26:48,486 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/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt" "/tmp/tmpg3zilamp/inter_no_balanced.cool" 2021-09-28 02:31:10,904 INFO SimpleSubprocess MakeCool - 0:04:22 2021-09-28 02:31:10,904 DEBUG SimpleSubprocess cp "/tmp/tmpg3zilamp/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-28 02:31:10,979 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 02:31:10,990 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt 2021-09-28 02:31:10,990 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-28 02:31:10,990 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 02:31:10,990 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 02:31:10,990 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-28 02:31:10,991 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/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt" "/tmp/tmpymri6aaw/inter_no_balanced.cool" 2021-09-28 02:35:29,333 INFO SimpleSubprocess MakeCool - 0:04:18 2021-09-28 02:35:29,333 DEBUG SimpleSubprocess cp "/tmp/tmpymri6aaw/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-28 02:35:29,407 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 02:35:29,417 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt 2021-09-28 02:35:29,417 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-28 02:35:29,417 INFO Pairs2Cool Genome assembly: mm10 2021-09-28 02:35:29,417 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 02:35:29,417 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-28 02:35:29,441 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/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt" "/tmp/tmpyrcgrqpr/inter_no_balanced.cool" 2021-09-28 02:39:38,845 INFO SimpleSubprocess MakeCool - 0:04:09 2021-09-28 02:39:38,845 DEBUG SimpleSubprocess cp "/tmp/tmpyrcgrqpr/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-28 02:39:38,907 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 02:39:39,065 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-28 02:39:39,065 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_5kb.cool 2021-09-28 02:39:39,066 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-28 02:39:39,120 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpmxfqotzh/inter.cool" 2021-09-28 02:39:39,223 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 02:39:39,223 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpmxfqotzh/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-28 02:39:59,254 INFO SimpleSubprocess NormalizeCool - 0:00:20 2021-09-28 02:39:59,255 DEBUG SimpleSubprocess cp "/tmp/tmpmxfqotzh/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_5kb.cool" 2021-09-28 02:39:59,350 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 02:39:59,381 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-28 02:39:59,381 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_10kb.cool 2021-09-28 02:39:59,381 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-28 02:39:59,381 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpo42xe8ur/inter.cool" 2021-09-28 02:39:59,472 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 02:39:59,473 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpo42xe8ur/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-28 02:40:13,616 INFO SimpleSubprocess NormalizeCool - 0:00:14 2021-09-28 02:40:13,617 DEBUG SimpleSubprocess cp "/tmp/tmpo42xe8ur/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_10kb.cool" 2021-09-28 02:40:13,708 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 02:40:13,721 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-28 02:40:13,722 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_20kb.cool 2021-09-28 02:40:13,722 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-28 02:40:13,791 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp603nkvmg/inter.cool" 2021-09-28 02:40:13,871 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 02:40:13,872 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp603nkvmg/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-28 02:40:23,221 INFO SimpleSubprocess NormalizeCool - 0:00:09 2021-09-28 02:40:23,221 DEBUG SimpleSubprocess cp "/tmp/tmp603nkvmg/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_20kb.cool" 2021-09-28 02:40:23,302 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 02:40:23,314 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-28 02:40:23,314 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_25kb.cool 2021-09-28 02:40:23,314 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-28 02:40:23,335 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpcayyau5r/inter.cool" 2021-09-28 02:40:23,409 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 02:40:23,409 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpcayyau5r/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-28 02:40:31,844 INFO SimpleSubprocess NormalizeCool - 0:00:08 2021-09-28 02:40:31,845 DEBUG SimpleSubprocess cp "/tmp/tmpcayyau5r/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_25kb.cool" 2021-09-28 02:40:31,919 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 02:40:31,929 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-28 02:40:31,929 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_50kb.cool 2021-09-28 02:40:31,929 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-28 02:40:31,953 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpmpfphj_k/inter.cool" 2021-09-28 02:40:32,015 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 02:40:32,015 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpmpfphj_k/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-28 02:40:36,791 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-09-28 02:40:36,791 DEBUG SimpleSubprocess cp "/tmp/tmpmpfphj_k/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_50kb.cool" 2021-09-28 02:40:36,853 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 02:40:36,880 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/vector.txt 2021-09-28 02:40:36,886 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-28 02:40:36,887 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_5kb.cool 2021-09-28 02:40:36,887 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/vector.txt 2021-09-28 02:40:36,887 INFO AddWeight Chromosome: chr5 2021-09-28 02:40:36,887 INFO AddWeight Resolution [bp]: 5000 2021-09-28 02:40:37,021 INFO AddWeight AddWeight successfully finished 2021-09-28 02:40:37,021 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_10kb.cool 2021-09-28 02:40:37,021 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/vector.txt 2021-09-28 02:40:37,022 INFO AddWeight Chromosome: chr5 2021-09-28 02:40:37,022 INFO AddWeight Resolution [bp]: 10000 2021-09-28 02:40:37,065 INFO AddWeight AddWeight successfully finished 2021-09-28 02:40:37,066 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_20kb.cool 2021-09-28 02:40:37,066 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/vector.txt 2021-09-28 02:40:37,066 INFO AddWeight Chromosome: chr5 2021-09-28 02:40:37,066 INFO AddWeight Resolution [bp]: 20000 2021-09-28 02:40:37,095 INFO AddWeight AddWeight successfully finished 2021-09-28 02:40:37,095 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_25kb.cool 2021-09-28 02:40:37,095 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/vector.txt 2021-09-28 02:40:37,095 INFO AddWeight Chromosome: chr5 2021-09-28 02:40:37,095 INFO AddWeight Resolution [bp]: 25000 2021-09-28 02:40:37,121 INFO AddWeight AddWeight successfully finished 2021-09-28 02:40:37,122 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_50kb.cool 2021-09-28 02:40:37,122 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/vector.txt 2021-09-28 02:40:37,122 INFO AddWeight Chromosome: chr5 2021-09-28 02:40:37,122 INFO AddWeight Resolution [bp]: 50000 2021-09-28 02:40:37,142 INFO AddWeight AddWeight successfully finished 2021-09-28 02:40:37,144 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter.hic 2021-09-28 02:40:37,144 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_norm.hic 2021-09-28 02:40:37,145 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/vector.txt 2021-09-28 02:40:37,145 INFO Vector2HiC Threads: 10 2021-09-28 02:40:37,169 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter.hic" "/tmp/tmppf4z644p/inter.hic" 2021-09-28 02:40:38,093 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-28 02:40:38,094 INFO Vector2HiC Vector: vector c-tale_normalization chr5 5000 BP 2021-09-28 02:40:38,095 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmppf4z644p/inter.hic" "/tmp/tmppf4z644p/vector.txt" 2021-09-28 02:40:43,244 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-09-28 02:40:43,245 INFO Vector2HiC Vector: vector c-tale_normalization chr5 10000 BP 2021-09-28 02:40:43,245 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmppf4z644p/inter.hic" "/tmp/tmppf4z644p/vector.txt" 2021-09-28 02:40:48,015 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-28 02:40:48,015 INFO Vector2HiC Vector: vector c-tale_normalization chr5 20000 BP 2021-09-28 02:40:48,015 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmppf4z644p/inter.hic" "/tmp/tmppf4z644p/vector.txt" 2021-09-28 02:40:52,040 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-28 02:40:52,040 INFO Vector2HiC Vector: vector c-tale_normalization chr5 25000 BP 2021-09-28 02:40:52,040 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmppf4z644p/inter.hic" "/tmp/tmppf4z644p/vector.txt" 2021-09-28 02:40:56,378 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-28 02:40:56,378 INFO Vector2HiC Vector: vector c-tale_normalization chr5 50000 BP 2021-09-28 02:40:56,379 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmppf4z644p/inter.hic" "/tmp/tmppf4z644p/vector.txt" 2021-09-28 02:41:00,916 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-28 02:41:00,916 DEBUG SimpleSubprocess cp "/tmp/tmppf4z644p/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_norm.hic" 2021-09-28 02:41:01,528 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-28 02:41:01,633 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/merged_nodups.txt" 2021-09-28 02:45:14,439 INFO SimpleSubprocess CopyResult - 0:04:12 2021-09-28 02:45:14,477 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter.pairs.txt" 2021-09-28 02:45:53,775 INFO SimpleSubprocess CopyResult - 0:00:39 2021-09-28 02:45:53,775 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/vector.txt" 2021-09-28 02:45:53,827 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 02:45:53,827 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter.hic" 2021-09-28 02:46:00,263 INFO SimpleSubprocess CopyResult - 0:00:06 2021-09-28 02:46:00,263 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter_statistics.txt" 2021-09-28 02:46:00,366 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 02:46:00,367 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter_no_balanced_5kb.cool" 2021-09-28 02:46:01,285 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 02:46:01,285 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter_5kb.cool" 2021-09-28 02:46:02,031 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 02:46:02,032 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter_no_balanced_10kb.cool" 2021-09-28 02:46:03,122 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-28 02:46:03,123 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter_10kb.cool" 2021-09-28 02:46:03,775 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 02:46:03,775 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter_no_balanced_20kb.cool" 2021-09-28 02:46:04,876 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-28 02:46:04,876 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter_20kb.cool" 2021-09-28 02:46:05,416 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 02:46:05,416 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter_no_balanced_25kb.cool" 2021-09-28 02:46:06,009 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 02:46:06,010 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter_25kb.cool" 2021-09-28 02:46:06,657 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 02:46:06,657 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter_no_balanced_50kb.cool" 2021-09-28 02:46:07,180 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 02:46:07,181 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/inter_50kb.cool" 2021-09-28 02:46:07,536 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-28 02:46:07,660 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284503-SRR8284504/__temp__" 2021-09-28 02:46:45,216 INFO SimpleSubprocess RemoveTemp - 0:00:37 2021-09-28 02:46:45,217 INFO BenchmarkPipeline 'SRR8284503-SRR8284504' FINISHED, SUMMARY TIME - 1 day, 1:25:13