2021-09-02 16:43:12,371 INFO BenchmarkPipeline --- START PROCESSING 'SRR5855094-SRR5855095' --- 2021-09-02 16:43:12,371 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855094.sra 2021-09-02 16:43:12,371 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__ 2021-09-02 16:43:12,371 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpwvcgpxu9 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855094.sra" 2021-09-02 16:52:25,912 INFO SimpleSubprocess Sra2FastQ - 0:09:13 2021-09-02 16:52:25,912 DEBUG SimpleSubprocess gzip /tmp/tmpwvcgpxu9/* 2021-09-02 17:12:50,964 INFO SimpleSubprocess GZipFastQ - 0:20:25 2021-09-02 17:12:50,965 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/fastq"; mv /tmp/tmpwvcgpxu9/SRR5855094_1.fastq.gz /tmp/tmpwvcgpxu9/SRR5855094_R1.fastq.gz; mv /tmp/tmpwvcgpxu9/SRR5855094_2.fastq.gz /tmp/tmpwvcgpxu9/SRR5855094_R2.fastq.gz; cp /tmp/tmpwvcgpxu9/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/fastq" 2021-09-02 17:12:54,922 INFO SimpleSubprocess CopyFiles - 0:00:03 2021-09-02 17:12:55,653 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855095.sra 2021-09-02 17:12:55,653 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__ 2021-09-02 17:12:55,653 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp8tumbjb2 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855095.sra" 2021-09-02 17:22:39,568 INFO SimpleSubprocess Sra2FastQ - 0:09:43 2021-09-02 17:22:39,569 DEBUG SimpleSubprocess gzip /tmp/tmp8tumbjb2/* 2021-09-02 17:43:50,908 INFO SimpleSubprocess GZipFastQ - 0:21:11 2021-09-02 17:43:50,917 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/fastq"; mv /tmp/tmp8tumbjb2/SRR5855095_1.fastq.gz /tmp/tmp8tumbjb2/SRR5855095_R1.fastq.gz; mv /tmp/tmp8tumbjb2/SRR5855095_2.fastq.gz /tmp/tmp8tumbjb2/SRR5855095_R2.fastq.gz; cp /tmp/tmp8tumbjb2/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/fastq" 2021-09-02 17:43:54,980 INFO SimpleSubprocess CopyFiles - 0:00:04 2021-09-02 17:43:55,568 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__ 2021-09-02 17:43:55,568 INFO Juicer Genome assembly: mm10 2021-09-02 17:43:55,568 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-02 17:43:55,568 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-02 17:43:55,568 INFO Juicer Enzyme: DpnII 2021-09-02 17:43:55,568 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-02 17:43:55,568 INFO Juicer Threads: 10 2021-09-02 17:43:55,568 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/splits" 2021-09-02 17:43:55,577 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-02 17:43:55,578 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/SRR5855094-SRR5855095/__temp__" 2021-09-02 23:51:00,627 INFO SimpleSubprocess Juicer - 6:07:05 2021-09-02 23:51:00,671 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/SRR5855094-SRR5855095/__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/SRR5855094-SRR5855095/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/splits/SRR5855094_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/splits/SRR5855094_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/splits/SRR5855094.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/splits/SRR5855094.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/splits/SRR5855095_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/splits/SRR5855095_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/splits/SRR5855095.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/splits/SRR5855095.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 [2021-09-02T21:38:53,133] [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 [2021-09-02T22:52:22,545] [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/SRR5855094-SRR5855095/__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 [2021-09-02T23:51:00,130] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__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/SRR5855094-SRR5855095/__temp__/aligned for results 2021-09-02 23:51:00,752 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/merged_nodups.txt 2021-09-02 23:51:00,752 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt 2021-09-02 23:51:00,752 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpuusm_mst/inter.pairs.txt" 2021-09-02 23:52:33,618 INFO SimpleSubprocess MakeInterPairs - 0:01:32 2021-09-02 23:52:33,618 DEBUG SimpleSubprocess cp "/tmp/tmpuusm_mst/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt" 2021-09-02 23:52:36,092 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-02 23:52:36,453 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt 2021-09-02 23:52:36,453 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-02 23:52:36,454 INFO Pairs2Cool Genome assembly: mm10 2021-09-02 23:52:36,454 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-02 23:52:36,454 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-02 23:52:36,454 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/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt" "/tmp/tmpshsozafu/inter_no_balanced.cool" 2021-09-02 23:56:23,345 INFO SimpleSubprocess MakeCool - 0:03:46 2021-09-02 23:56:23,345 DEBUG SimpleSubprocess cp "/tmp/tmpshsozafu/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-02 23:56:23,471 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-02 23:56:23,486 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt 2021-09-02 23:56:23,486 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-02 23:56:23,486 INFO Pairs2Cool Genome assembly: mm10 2021-09-02 23:56:23,486 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-02 23:56:23,487 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-02 23:56:23,487 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/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt" "/tmp/tmpjkvqed2k/inter_no_balanced.cool" 2021-09-02 23:59:50,351 INFO SimpleSubprocess MakeCool - 0:03:26 2021-09-02 23:59:50,351 DEBUG SimpleSubprocess cp "/tmp/tmpjkvqed2k/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-02 23:59:50,451 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-02 23:59:50,465 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt 2021-09-02 23:59:50,465 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-02 23:59:50,465 INFO Pairs2Cool Genome assembly: mm10 2021-09-02 23:59:50,465 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-02 23:59:50,465 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-02 23:59:50,466 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/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt" "/tmp/tmp1_xczrit/inter_no_balanced.cool" 2021-09-03 00:03:04,781 INFO SimpleSubprocess MakeCool - 0:03:14 2021-09-03 00:03:04,781 DEBUG SimpleSubprocess cp "/tmp/tmp1_xczrit/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-03 00:03:04,877 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 00:03:04,890 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt 2021-09-03 00:03:04,890 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-03 00:03:04,890 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 00:03:04,890 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 00:03:04,890 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-03 00:03:04,890 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/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt" "/tmp/tmp4u_ii431/inter_no_balanced.cool" 2021-09-03 00:06:11,016 INFO SimpleSubprocess MakeCool - 0:03:06 2021-09-03 00:06:11,016 DEBUG SimpleSubprocess cp "/tmp/tmp4u_ii431/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-03 00:06:11,096 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 00:06:11,108 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt 2021-09-03 00:06:11,108 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-03 00:06:11,108 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 00:06:11,108 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 00:06:11,108 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-03 00:06:11,108 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/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt" "/tmp/tmpe90xl8kg/inter_no_balanced.cool" 2021-09-03 00:09:04,145 INFO SimpleSubprocess MakeCool - 0:02:53 2021-09-03 00:09:04,145 DEBUG SimpleSubprocess cp "/tmp/tmpe90xl8kg/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-03 00:09:04,213 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 00:09:04,245 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-03 00:09:04,245 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_5kb.cool 2021-09-03 00:09:04,245 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 00:09:04,246 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp5kspycd7/inter.cool" 2021-09-03 00:09:04,364 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 00:09:04,364 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp5kspycd7/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 00:09:20,015 INFO SimpleSubprocess NormalizeCool - 0:00:15 2021-09-03 00:09:20,015 DEBUG SimpleSubprocess cp "/tmp/tmp5kspycd7/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_5kb.cool" 2021-09-03 00:09:20,134 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 00:09:20,153 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-03 00:09:20,153 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_10kb.cool 2021-09-03 00:09:20,153 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 00:09:20,153 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpr42v9ro0/inter.cool" 2021-09-03 00:09:20,256 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 00:09:20,256 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpr42v9ro0/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 00:09:37,611 INFO SimpleSubprocess NormalizeCool - 0:00:17 2021-09-03 00:09:37,611 DEBUG SimpleSubprocess cp "/tmp/tmpr42v9ro0/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_10kb.cool" 2021-09-03 00:09:37,714 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 00:09:37,729 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-03 00:09:37,729 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_20kb.cool 2021-09-03 00:09:37,729 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 00:09:37,729 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpu8e00ri1/inter.cool" 2021-09-03 00:09:37,816 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 00:09:37,816 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpu8e00ri1/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 00:09:40,808 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-03 00:09:40,808 DEBUG SimpleSubprocess cp "/tmp/tmpu8e00ri1/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_20kb.cool" 2021-09-03 00:09:40,902 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 00:09:40,915 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-03 00:09:40,915 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_25kb.cool 2021-09-03 00:09:40,915 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 00:09:40,915 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpsdqstpbv/inter.cool" 2021-09-03 00:09:41,001 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 00:09:41,001 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpsdqstpbv/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 00:09:43,836 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-03 00:09:43,837 DEBUG SimpleSubprocess cp "/tmp/tmpsdqstpbv/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_25kb.cool" 2021-09-03 00:09:43,916 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 00:09:43,927 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-03 00:09:43,928 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_50kb.cool 2021-09-03 00:09:43,928 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 00:09:43,928 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp9cpsbymo/inter.cool" 2021-09-03 00:09:43,993 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 00:09:43,993 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp9cpsbymo/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 00:09:46,272 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-03 00:09:46,273 DEBUG SimpleSubprocess cp "/tmp/tmp9cpsbymo/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_50kb.cool" 2021-09-03 00:09:46,338 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 00:09:46,349 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/vector.txt 2021-09-03 00:09:46,358 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-03 00:09:46,358 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_5kb.cool 2021-09-03 00:09:46,358 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/vector.txt 2021-09-03 00:09:46,358 INFO AddWeight Chromosome: chr2 2021-09-03 00:09:46,358 INFO AddWeight Resolution [bp]: 5000 2021-09-03 00:09:46,477 INFO AddWeight AddWeight successfully finished 2021-09-03 00:09:46,477 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_10kb.cool 2021-09-03 00:09:46,477 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/vector.txt 2021-09-03 00:09:46,478 INFO AddWeight Chromosome: chr2 2021-09-03 00:09:46,478 INFO AddWeight Resolution [bp]: 10000 2021-09-03 00:09:46,522 INFO AddWeight AddWeight successfully finished 2021-09-03 00:09:46,523 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_20kb.cool 2021-09-03 00:09:46,523 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/vector.txt 2021-09-03 00:09:46,523 INFO AddWeight Chromosome: chr2 2021-09-03 00:09:46,523 INFO AddWeight Resolution [bp]: 20000 2021-09-03 00:09:46,562 INFO AddWeight AddWeight successfully finished 2021-09-03 00:09:46,562 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_25kb.cool 2021-09-03 00:09:46,562 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/vector.txt 2021-09-03 00:09:46,562 INFO AddWeight Chromosome: chr2 2021-09-03 00:09:46,562 INFO AddWeight Resolution [bp]: 25000 2021-09-03 00:09:46,594 INFO AddWeight AddWeight successfully finished 2021-09-03 00:09:46,594 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_50kb.cool 2021-09-03 00:09:46,595 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/vector.txt 2021-09-03 00:09:46,595 INFO AddWeight Chromosome: chr2 2021-09-03 00:09:46,595 INFO AddWeight Resolution [bp]: 50000 2021-09-03 00:09:46,618 INFO AddWeight AddWeight successfully finished 2021-09-03 00:09:46,620 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter.hic 2021-09-03 00:09:46,620 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_norm.hic 2021-09-03 00:09:46,620 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/vector.txt 2021-09-03 00:09:46,620 INFO Vector2HiC Threads: 10 2021-09-03 00:09:46,648 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter.hic" "/tmp/tmpzl8idmqg/inter.hic" 2021-09-03 00:09:47,447 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 00:09:47,447 INFO Vector2HiC Vector: vector c-tale_normalization chr2 5000 BP 2021-09-03 00:09:47,449 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpzl8idmqg/inter.hic" "/tmp/tmpzl8idmqg/vector.txt" 2021-09-03 00:09:52,297 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-03 00:09:52,298 INFO Vector2HiC Vector: vector c-tale_normalization chr2 10000 BP 2021-09-03 00:09:52,299 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpzl8idmqg/inter.hic" "/tmp/tmpzl8idmqg/vector.txt" 2021-09-03 00:09:56,400 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-03 00:09:56,400 INFO Vector2HiC Vector: vector c-tale_normalization chr2 20000 BP 2021-09-03 00:09:56,401 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpzl8idmqg/inter.hic" "/tmp/tmpzl8idmqg/vector.txt" 2021-09-03 00:09:59,927 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-03 00:09:59,927 INFO Vector2HiC Vector: vector c-tale_normalization chr2 25000 BP 2021-09-03 00:09:59,928 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpzl8idmqg/inter.hic" "/tmp/tmpzl8idmqg/vector.txt" 2021-09-03 00:10:03,948 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-03 00:10:03,948 INFO Vector2HiC Vector: vector c-tale_normalization chr2 50000 BP 2021-09-03 00:10:04,050 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpzl8idmqg/inter.hic" "/tmp/tmpzl8idmqg/vector.txt" 2021-09-03 00:10:08,073 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-03 00:10:08,073 DEBUG SimpleSubprocess cp "/tmp/tmpzl8idmqg/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_norm.hic" 2021-09-03 00:10:08,991 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 00:10:09,918 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/merged_nodups.txt" 2021-09-03 00:11:40,815 INFO SimpleSubprocess CopyResult - 0:01:30 2021-09-03 00:11:40,832 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter.pairs.txt" 2021-09-03 00:12:00,655 INFO SimpleSubprocess CopyResult - 0:00:19 2021-09-03 00:12:00,655 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/vector.txt" 2021-09-03 00:12:00,764 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 00:12:00,764 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter.hic" 2021-09-03 00:12:09,460 INFO SimpleSubprocess CopyResult - 0:00:08 2021-09-03 00:12:09,460 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter_statistics.txt" 2021-09-03 00:12:09,470 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 00:12:09,470 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter_no_balanced_5kb.cool" 2021-09-03 00:12:11,655 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-03 00:12:11,656 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter_5kb.cool" 2021-09-03 00:12:12,837 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 00:12:12,837 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter_no_balanced_10kb.cool" 2021-09-03 00:12:13,840 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 00:12:13,841 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter_10kb.cool" 2021-09-03 00:12:14,595 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 00:12:14,595 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter_no_balanced_20kb.cool" 2021-09-03 00:12:15,742 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 00:12:15,742 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter_20kb.cool" 2021-09-03 00:12:16,324 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 00:12:16,324 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter_no_balanced_25kb.cool" 2021-09-03 00:12:16,855 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 00:12:16,855 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter_25kb.cool" 2021-09-03 00:12:17,743 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 00:12:17,743 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter_no_balanced_50kb.cool" 2021-09-03 00:12:18,374 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 00:12:18,375 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/inter_50kb.cool" 2021-09-03 00:12:19,088 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 00:12:19,379 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855094-SRR5855095/__temp__" 2021-09-03 00:12:26,327 INFO SimpleSubprocess RemoveTemp - 0:00:06 2021-09-03 00:12:26,327 INFO BenchmarkPipeline 'SRR5855094-SRR5855095' FINISHED, SUMMARY TIME - 7:29:13