2021-09-03 00:12:26,379 INFO BenchmarkPipeline --- START PROCESSING 'SRR5855098-SRR5855099' --- 2021-09-03 00:12:26,379 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855098.sra 2021-09-03 00:12:26,379 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__ 2021-09-03 00:12:26,379 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmphrtdrcaq "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855098.sra" 2021-09-03 00:21:19,051 INFO SimpleSubprocess Sra2FastQ - 0:08:52 2021-09-03 00:21:19,051 DEBUG SimpleSubprocess gzip /tmp/tmphrtdrcaq/* 2021-09-03 00:42:15,031 INFO SimpleSubprocess GZipFastQ - 0:20:55 2021-09-03 00:42:15,032 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/fastq"; mv /tmp/tmphrtdrcaq/SRR5855098_2.fastq.gz /tmp/tmphrtdrcaq/SRR5855098_R2.fastq.gz; mv /tmp/tmphrtdrcaq/SRR5855098_1.fastq.gz /tmp/tmphrtdrcaq/SRR5855098_R1.fastq.gz; cp /tmp/tmphrtdrcaq/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/fastq" 2021-09-03 00:42:19,074 INFO SimpleSubprocess CopyFiles - 0:00:04 2021-09-03 00:42:19,630 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855099.sra 2021-09-03 00:42:19,630 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__ 2021-09-03 00:42:19,630 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp51ztfi8e "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR5855099.sra" 2021-09-03 00:51:44,101 INFO SimpleSubprocess Sra2FastQ - 0:09:24 2021-09-03 00:51:44,101 DEBUG SimpleSubprocess gzip /tmp/tmp51ztfi8e/* 2021-09-03 01:14:03,995 INFO SimpleSubprocess GZipFastQ - 0:22:19 2021-09-03 01:14:03,996 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/fastq"; mv /tmp/tmp51ztfi8e/SRR5855099_2.fastq.gz /tmp/tmp51ztfi8e/SRR5855099_R2.fastq.gz; mv /tmp/tmp51ztfi8e/SRR5855099_1.fastq.gz /tmp/tmp51ztfi8e/SRR5855099_R1.fastq.gz; cp /tmp/tmp51ztfi8e/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/fastq" 2021-09-03 01:14:08,049 INFO SimpleSubprocess CopyFiles - 0:00:04 2021-09-03 01:14:08,618 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__ 2021-09-03 01:14:08,618 INFO Juicer Genome assembly: mm10 2021-09-03 01:14:08,618 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-03 01:14:08,618 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 01:14:08,618 INFO Juicer Enzyme: DpnII 2021-09-03 01:14:08,618 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-03 01:14:08,619 INFO Juicer Threads: 10 2021-09-03 01:14:08,619 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/splits" 2021-09-03 01:14:08,628 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-03 01:14:08,628 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/SRR5855098-SRR5855099/__temp__" 2021-09-03 07:37:45,554 INFO SimpleSubprocess Juicer - 6:23:36 2021-09-03 07:37:45,571 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/SRR5855098-SRR5855099/__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/SRR5855098-SRR5855099/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/splits/SRR5855098_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/splits/SRR5855098_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/splits/SRR5855098.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/splits/SRR5855098.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/splits/SRR5855099_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/splits/SRR5855099_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/splits/SRR5855099.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/splits/SRR5855099.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 [2021-09-03T05:14:34,085] [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 [2021-09-03T06:41:29,874] [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/SRR5855098-SRR5855099/__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 [2021-09-03T07:37:45,005] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__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/SRR5855098-SRR5855099/__temp__/aligned for results 2021-09-03 07:37:45,616 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/merged_nodups.txt 2021-09-03 07:37:45,616 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt 2021-09-03 07:37:45,616 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpqvq1g0oq/inter.pairs.txt" 2021-09-03 07:39:22,601 INFO SimpleSubprocess MakeInterPairs - 0:01:36 2021-09-03 07:39:22,601 DEBUG SimpleSubprocess cp "/tmp/tmpqvq1g0oq/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt" 2021-09-03 07:39:25,103 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-03 07:39:25,594 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt 2021-09-03 07:39:25,594 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-03 07:39:25,594 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 07:39:25,595 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 07:39:25,595 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-03 07:39:25,595 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/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt" "/tmp/tmp1233qt56/inter_no_balanced.cool" 2021-09-03 07:43:27,136 INFO SimpleSubprocess MakeCool - 0:04:01 2021-09-03 07:43:27,136 DEBUG SimpleSubprocess cp "/tmp/tmp1233qt56/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-03 07:43:27,261 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 07:43:27,278 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt 2021-09-03 07:43:27,278 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-03 07:43:27,278 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 07:43:27,278 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 07:43:27,279 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-03 07:43:27,279 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/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt" "/tmp/tmpeui4mhpo/inter_no_balanced.cool" 2021-09-03 07:47:08,837 INFO SimpleSubprocess MakeCool - 0:03:41 2021-09-03 07:47:08,837 DEBUG SimpleSubprocess cp "/tmp/tmpeui4mhpo/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-03 07:47:08,943 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 07:47:08,957 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt 2021-09-03 07:47:08,957 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-03 07:47:08,958 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 07:47:08,958 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 07:47:08,958 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-03 07:47:08,958 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/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt" "/tmp/tmp50hgg6pq/inter_no_balanced.cool" 2021-09-03 07:50:35,850 INFO SimpleSubprocess MakeCool - 0:03:26 2021-09-03 07:50:35,850 DEBUG SimpleSubprocess cp "/tmp/tmp50hgg6pq/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-03 07:50:35,950 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 07:50:35,962 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt 2021-09-03 07:50:35,963 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-03 07:50:35,963 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 07:50:35,963 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 07:50:35,963 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-03 07:50:35,963 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/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt" "/tmp/tmpvmuqbwho/inter_no_balanced.cool" 2021-09-03 07:54:00,597 INFO SimpleSubprocess MakeCool - 0:03:24 2021-09-03 07:54:00,597 DEBUG SimpleSubprocess cp "/tmp/tmpvmuqbwho/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-03 07:54:00,689 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 07:54:00,703 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt 2021-09-03 07:54:00,703 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-03 07:54:00,703 INFO Pairs2Cool Genome assembly: mm10 2021-09-03 07:54:00,703 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-03 07:54:00,703 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-03 07:54:00,703 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/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt" "/tmp/tmpd6luxxl7/inter_no_balanced.cool" 2021-09-03 07:57:05,435 INFO SimpleSubprocess MakeCool - 0:03:04 2021-09-03 07:57:05,436 DEBUG SimpleSubprocess cp "/tmp/tmpd6luxxl7/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-03 07:57:05,510 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 07:57:05,522 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-03 07:57:05,522 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_5kb.cool 2021-09-03 07:57:05,522 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 07:57:05,522 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp9sw917ik/inter.cool" 2021-09-03 07:57:05,655 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 07:57:05,655 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp9sw917ik/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 07:57:21,588 INFO SimpleSubprocess NormalizeCool - 0:00:15 2021-09-03 07:57:21,588 DEBUG SimpleSubprocess cp "/tmp/tmp9sw917ik/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_5kb.cool" 2021-09-03 07:57:21,711 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 07:57:21,729 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-03 07:57:21,729 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_10kb.cool 2021-09-03 07:57:21,730 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 07:57:21,730 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpvrspet6_/inter.cool" 2021-09-03 07:57:21,839 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 07:57:21,840 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpvrspet6_/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 07:57:40,020 INFO SimpleSubprocess NormalizeCool - 0:00:18 2021-09-03 07:57:40,020 DEBUG SimpleSubprocess cp "/tmp/tmpvrspet6_/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_10kb.cool" 2021-09-03 07:57:40,136 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 07:57:40,153 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-03 07:57:40,153 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_20kb.cool 2021-09-03 07:57:40,153 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 07:57:40,153 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmprl7mi32x/inter.cool" 2021-09-03 07:57:40,253 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 07:57:40,253 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmprl7mi32x/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 07:57:43,547 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-03 07:57:43,547 DEBUG SimpleSubprocess cp "/tmp/tmprl7mi32x/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_20kb.cool" 2021-09-03 07:57:43,645 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 07:57:43,660 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-03 07:57:43,660 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_25kb.cool 2021-09-03 07:57:43,660 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 07:57:43,661 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpce_ng20h/inter.cool" 2021-09-03 07:57:43,753 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 07:57:43,753 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpce_ng20h/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 07:57:46,846 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-03 07:57:46,847 DEBUG SimpleSubprocess cp "/tmp/tmpce_ng20h/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_25kb.cool" 2021-09-03 07:57:46,936 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 07:57:46,950 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-03 07:57:46,950 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_50kb.cool 2021-09-03 07:57:46,950 INFO CTaleNormalize Capture: chr2:70,945,000-81,015,000 2021-09-03 07:57:46,951 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp5qz4iyai/inter.cool" 2021-09-03 07:57:47,026 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 07:57:47,026 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp5qz4iyai/inter.cool" "chr2:70,945,000-81,015,000" 2021-09-03 07:57:49,583 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-03 07:57:49,583 DEBUG SimpleSubprocess cp "/tmp/tmp5qz4iyai/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_50kb.cool" 2021-09-03 07:57:49,658 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 07:57:49,671 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/vector.txt 2021-09-03 07:57:49,678 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-03 07:57:49,679 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_5kb.cool 2021-09-03 07:57:49,679 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/vector.txt 2021-09-03 07:57:49,679 INFO AddWeight Chromosome: chr2 2021-09-03 07:57:49,679 INFO AddWeight Resolution [bp]: 5000 2021-09-03 07:57:49,809 INFO AddWeight AddWeight successfully finished 2021-09-03 07:57:49,809 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_10kb.cool 2021-09-03 07:57:49,810 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/vector.txt 2021-09-03 07:57:49,810 INFO AddWeight Chromosome: chr2 2021-09-03 07:57:49,810 INFO AddWeight Resolution [bp]: 10000 2021-09-03 07:57:49,859 INFO AddWeight AddWeight successfully finished 2021-09-03 07:57:49,860 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_20kb.cool 2021-09-03 07:57:49,860 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/vector.txt 2021-09-03 07:57:49,860 INFO AddWeight Chromosome: chr2 2021-09-03 07:57:49,860 INFO AddWeight Resolution [bp]: 20000 2021-09-03 07:57:49,901 INFO AddWeight AddWeight successfully finished 2021-09-03 07:57:49,901 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_25kb.cool 2021-09-03 07:57:49,901 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/vector.txt 2021-09-03 07:57:49,902 INFO AddWeight Chromosome: chr2 2021-09-03 07:57:49,902 INFO AddWeight Resolution [bp]: 25000 2021-09-03 07:57:49,938 INFO AddWeight AddWeight successfully finished 2021-09-03 07:57:49,938 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_50kb.cool 2021-09-03 07:57:49,939 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/vector.txt 2021-09-03 07:57:49,939 INFO AddWeight Chromosome: chr2 2021-09-03 07:57:49,939 INFO AddWeight Resolution [bp]: 50000 2021-09-03 07:57:49,964 INFO AddWeight AddWeight successfully finished 2021-09-03 07:57:49,966 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter.hic 2021-09-03 07:57:49,966 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_norm.hic 2021-09-03 07:57:49,966 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/vector.txt 2021-09-03 07:57:49,966 INFO Vector2HiC Threads: 10 2021-09-03 07:57:49,998 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter.hic" "/tmp/tmpa0x49ydc/inter.hic" 2021-09-03 07:57:50,888 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-03 07:57:50,888 INFO Vector2HiC Vector: vector c-tale_normalization chr2 5000 BP 2021-09-03 07:57:50,890 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpa0x49ydc/inter.hic" "/tmp/tmpa0x49ydc/vector.txt" 2021-09-03 07:57:56,142 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-09-03 07:57:56,143 INFO Vector2HiC Vector: vector c-tale_normalization chr2 10000 BP 2021-09-03 07:57:56,144 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpa0x49ydc/inter.hic" "/tmp/tmpa0x49ydc/vector.txt" 2021-09-03 07:58:00,331 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-03 07:58:00,331 INFO Vector2HiC Vector: vector c-tale_normalization chr2 20000 BP 2021-09-03 07:58:00,332 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpa0x49ydc/inter.hic" "/tmp/tmpa0x49ydc/vector.txt" 2021-09-03 07:58:04,002 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-03 07:58:04,003 INFO Vector2HiC Vector: vector c-tale_normalization chr2 25000 BP 2021-09-03 07:58:04,003 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpa0x49ydc/inter.hic" "/tmp/tmpa0x49ydc/vector.txt" 2021-09-03 07:58:08,018 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-03 07:58:08,018 INFO Vector2HiC Vector: vector c-tale_normalization chr2 50000 BP 2021-09-03 07:58:08,034 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpa0x49ydc/inter.hic" "/tmp/tmpa0x49ydc/vector.txt" 2021-09-03 07:58:12,006 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-03 07:58:12,007 DEBUG SimpleSubprocess cp "/tmp/tmpa0x49ydc/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_norm.hic" 2021-09-03 07:58:12,935 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-03 07:58:13,677 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/merged_nodups.txt" 2021-09-03 07:59:44,607 INFO SimpleSubprocess CopyResult - 0:01:30 2021-09-03 07:59:44,718 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter.pairs.txt" 2021-09-03 08:00:01,893 INFO SimpleSubprocess CopyResult - 0:00:17 2021-09-03 08:00:01,893 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/vector.txt" 2021-09-03 08:00:02,240 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 08:00:02,241 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter.hic" 2021-09-03 08:00:10,746 INFO SimpleSubprocess CopyResult - 0:00:08 2021-09-03 08:00:10,746 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter_statistics.txt" 2021-09-03 08:00:10,866 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 08:00:10,866 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter_no_balanced_5kb.cool" 2021-09-03 08:00:12,403 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 08:00:12,403 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter_5kb.cool" 2021-09-03 08:00:13,487 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 08:00:13,487 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter_no_balanced_10kb.cool" 2021-09-03 08:00:14,683 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 08:00:14,683 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter_10kb.cool" 2021-09-03 08:00:16,175 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 08:00:16,175 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter_no_balanced_20kb.cool" 2021-09-03 08:00:16,919 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 08:00:16,919 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter_20kb.cool" 2021-09-03 08:00:17,761 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-03 08:00:17,762 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter_no_balanced_25kb.cool" 2021-09-03 08:00:19,575 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 08:00:19,576 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter_25kb.cool" 2021-09-03 08:00:20,672 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 08:00:20,673 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter_no_balanced_50kb.cool" 2021-09-03 08:00:21,721 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 08:00:21,721 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/inter_50kb.cool" 2021-09-03 08:00:23,409 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-03 08:00:23,486 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR5855098-SRR5855099/__temp__" 2021-09-03 08:00:30,034 INFO SimpleSubprocess RemoveTemp - 0:00:06 2021-09-03 08:00:30,034 INFO BenchmarkPipeline 'SRR5855098-SRR5855099' FINISHED, SUMMARY TIME - 7:48:03