2021-09-28 20:40:38,138 INFO BenchmarkPipeline --- START PROCESSING 'SRR8453401-SRR8453402' --- 2021-09-28 20:40:38,139 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453401.sra 2021-09-28 20:40:38,139 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__ 2021-09-28 20:40:38,139 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp94pd1360 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453401.sra" 2021-09-28 20:46:55,494 INFO SimpleSubprocess Sra2FastQ - 0:06:17 2021-09-28 20:46:55,495 DEBUG SimpleSubprocess gzip /tmp/tmp94pd1360/* 2021-09-28 21:01:16,755 INFO SimpleSubprocess GZipFastQ - 0:14:21 2021-09-28 21:01:16,842 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/fastq"; mv /tmp/tmp94pd1360/SRR8453401_1.fastq.gz /tmp/tmp94pd1360/SRR8453401_R1.fastq.gz; mv /tmp/tmp94pd1360/SRR8453401_2.fastq.gz /tmp/tmp94pd1360/SRR8453401_R2.fastq.gz; cp /tmp/tmp94pd1360/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/fastq" 2021-09-28 21:01:19,604 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-28 21:01:19,973 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453402.sra 2021-09-28 21:01:19,973 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__ 2021-09-28 21:01:19,974 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpf_6y3_mh "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8453402.sra" 2021-09-28 21:21:14,202 INFO SimpleSubprocess Sra2FastQ - 0:19:54 2021-09-28 21:21:14,229 DEBUG SimpleSubprocess gzip /tmp/tmpf_6y3_mh/* 2021-09-28 22:07:23,619 INFO SimpleSubprocess GZipFastQ - 0:46:09 2021-09-28 22:07:23,620 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/fastq"; mv /tmp/tmpf_6y3_mh/SRR8453402_1.fastq.gz /tmp/tmpf_6y3_mh/SRR8453402_R1.fastq.gz; mv /tmp/tmpf_6y3_mh/SRR8453402_2.fastq.gz /tmp/tmpf_6y3_mh/SRR8453402_R2.fastq.gz; cp /tmp/tmpf_6y3_mh/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/fastq" 2021-09-28 22:07:34,697 INFO SimpleSubprocess CopyFiles - 0:00:11 2021-09-28 22:07:35,949 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__ 2021-09-28 22:07:35,949 INFO Juicer Genome assembly: mm10 2021-09-28 22:07:35,949 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-28 22:07:35,949 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-28 22:07:35,949 INFO Juicer Enzyme: DpnII 2021-09-28 22:07:35,949 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-28 22:07:35,949 INFO Juicer Threads: 10 2021-09-28 22:07:35,949 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/HIC_tmp" 2021-09-28 22:07:35,980 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-28 22:07:35,980 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/SRR8453401-SRR8453402/__temp__" 2021-09-29 05:45:02,677 INFO SimpleSubprocess Juicer - 7:37:26 2021-09-29 05:45:02,706 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/SRR8453401-SRR8453402/__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/SRR8453401-SRR8453402/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/splits/SRR8453401_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/splits/SRR8453401_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/splits/SRR8453401.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/splits/SRR8453401.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/splits/SRR8453402_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/splits/SRR8453402_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/splits/SRR8453402.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/splits/SRR8453402.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 [2021-09-29T04:33:45,140] [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 [2021-09-29T05:15:20,223] [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/SRR8453401-SRR8453402/__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 [2021-09-29T05:45:02,112] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__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/SRR8453401-SRR8453402/__temp__/aligned for results 2021-09-29 05:45:02,750 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/merged_nodups.txt 2021-09-29 05:45:02,750 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt 2021-09-29 05:45:02,750 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp_jfnzutu/inter.pairs.txt" 2021-09-29 05:46:36,718 INFO SimpleSubprocess MakeInterPairs - 0:01:33 2021-09-29 05:46:36,718 DEBUG SimpleSubprocess cp "/tmp/tmp_jfnzutu/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt" 2021-09-29 05:46:39,441 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-09-29 05:46:39,839 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt 2021-09-29 05:46:39,839 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-29 05:46:39,840 INFO Pairs2Cool Genome assembly: mm10 2021-09-29 05:46:39,840 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 05:46:39,840 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-29 05:46:39,878 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/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt" "/tmp/tmpfctg71lj/inter_no_balanced.cool" 2021-09-29 05:49:10,564 INFO SimpleSubprocess MakeCool - 0:02:30 2021-09-29 05:49:10,565 DEBUG SimpleSubprocess cp "/tmp/tmpfctg71lj/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-29 05:49:10,652 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 05:49:10,689 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt 2021-09-29 05:49:10,689 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-29 05:49:10,689 INFO Pairs2Cool Genome assembly: mm10 2021-09-29 05:49:10,689 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 05:49:10,689 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-29 05:49:10,689 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/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt" "/tmp/tmpiiul796x/inter_no_balanced.cool" 2021-09-29 05:51:25,893 INFO SimpleSubprocess MakeCool - 0:02:15 2021-09-29 05:51:25,893 DEBUG SimpleSubprocess cp "/tmp/tmpiiul796x/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-29 05:51:25,936 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 05:51:25,969 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt 2021-09-29 05:51:25,969 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-29 05:51:25,969 INFO Pairs2Cool Genome assembly: mm10 2021-09-29 05:51:25,969 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 05:51:25,969 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-29 05:51:25,969 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/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt" "/tmp/tmp_jphncol/inter_no_balanced.cool" 2021-09-29 05:53:37,143 INFO SimpleSubprocess MakeCool - 0:02:11 2021-09-29 05:53:37,143 DEBUG SimpleSubprocess cp "/tmp/tmp_jphncol/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-29 05:53:37,182 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 05:53:37,368 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt 2021-09-29 05:53:37,368 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-29 05:53:37,368 INFO Pairs2Cool Genome assembly: mm10 2021-09-29 05:53:37,368 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 05:53:37,368 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-29 05:53:37,369 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/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt" "/tmp/tmpku1hpocc/inter_no_balanced.cool" 2021-09-29 05:55:49,955 INFO SimpleSubprocess MakeCool - 0:02:12 2021-09-29 05:55:49,956 DEBUG SimpleSubprocess cp "/tmp/tmpku1hpocc/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-29 05:55:49,991 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 05:55:50,022 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt 2021-09-29 05:55:50,023 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-29 05:55:50,023 INFO Pairs2Cool Genome assembly: mm10 2021-09-29 05:55:50,023 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-29 05:55:50,023 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-29 05:55:50,023 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/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt" "/tmp/tmp59hu3rf2/inter_no_balanced.cool" 2021-09-29 05:57:54,618 INFO SimpleSubprocess MakeCool - 0:02:04 2021-09-29 05:57:54,619 DEBUG SimpleSubprocess cp "/tmp/tmp59hu3rf2/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-29 05:57:54,652 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 05:57:54,683 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-29 05:57:54,683 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_5kb.cool 2021-09-29 05:57:54,683 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-29 05:57:54,689 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmppqzd7uv1/inter.cool" 2021-09-29 05:57:54,742 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 05:57:54,742 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmppqzd7uv1/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-29 05:58:00,071 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-09-29 05:58:00,071 DEBUG SimpleSubprocess cp "/tmp/tmppqzd7uv1/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_5kb.cool" 2021-09-29 05:58:00,145 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 05:58:00,153 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-29 05:58:00,153 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_10kb.cool 2021-09-29 05:58:00,153 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-29 05:58:00,153 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpecat_sn0/inter.cool" 2021-09-29 05:58:00,198 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 05:58:00,199 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpecat_sn0/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-29 05:58:02,734 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-29 05:58:02,734 DEBUG SimpleSubprocess cp "/tmp/tmpecat_sn0/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_10kb.cool" 2021-09-29 05:58:02,780 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 05:58:02,786 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-29 05:58:02,786 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_20kb.cool 2021-09-29 05:58:02,786 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-29 05:58:02,787 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp4uyl2rp7/inter.cool" 2021-09-29 05:58:02,828 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 05:58:02,828 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp4uyl2rp7/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-29 05:58:04,827 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-29 05:58:04,827 DEBUG SimpleSubprocess cp "/tmp/tmp4uyl2rp7/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_20kb.cool" 2021-09-29 05:58:04,868 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 05:58:04,918 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-29 05:58:04,918 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_25kb.cool 2021-09-29 05:58:04,918 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-29 05:58:04,918 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpoctu_abw/inter.cool" 2021-09-29 05:58:04,957 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 05:58:04,957 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpoctu_abw/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-29 05:58:06,805 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-29 05:58:06,805 DEBUG SimpleSubprocess cp "/tmp/tmpoctu_abw/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_25kb.cool" 2021-09-29 05:58:06,844 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 05:58:06,849 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-29 05:58:06,849 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_50kb.cool 2021-09-29 05:58:06,849 INFO CTaleNormalize Capture: chr11:109,140,001-115,015,000 2021-09-29 05:58:06,849 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpo2fbwmxi/inter.cool" 2021-09-29 05:58:06,882 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 05:58:06,882 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpo2fbwmxi/inter.cool" "chr11:109,140,001-115,015,000" 2021-09-29 05:58:08,317 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-29 05:58:08,318 DEBUG SimpleSubprocess cp "/tmp/tmpo2fbwmxi/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_50kb.cool" 2021-09-29 05:58:08,351 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 05:58:08,357 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/vector.txt 2021-09-29 05:58:08,363 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-29 05:58:08,364 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_5kb.cool 2021-09-29 05:58:08,364 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/vector.txt 2021-09-29 05:58:08,364 INFO AddWeight Chromosome: chr11 2021-09-29 05:58:08,364 INFO AddWeight Resolution [bp]: 5000 2021-09-29 05:58:08,459 INFO AddWeight AddWeight successfully finished 2021-09-29 05:58:08,459 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_10kb.cool 2021-09-29 05:58:08,459 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/vector.txt 2021-09-29 05:58:08,459 INFO AddWeight Chromosome: chr11 2021-09-29 05:58:08,460 INFO AddWeight Resolution [bp]: 10000 2021-09-29 05:58:08,512 INFO AddWeight AddWeight successfully finished 2021-09-29 05:58:08,512 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_20kb.cool 2021-09-29 05:58:08,512 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/vector.txt 2021-09-29 05:58:08,512 INFO AddWeight Chromosome: chr11 2021-09-29 05:58:08,512 INFO AddWeight Resolution [bp]: 20000 2021-09-29 05:58:08,546 INFO AddWeight AddWeight successfully finished 2021-09-29 05:58:08,546 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_25kb.cool 2021-09-29 05:58:08,546 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/vector.txt 2021-09-29 05:58:08,546 INFO AddWeight Chromosome: chr11 2021-09-29 05:58:08,547 INFO AddWeight Resolution [bp]: 25000 2021-09-29 05:58:08,577 INFO AddWeight AddWeight successfully finished 2021-09-29 05:58:08,577 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_50kb.cool 2021-09-29 05:58:08,577 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/vector.txt 2021-09-29 05:58:08,577 INFO AddWeight Chromosome: chr11 2021-09-29 05:58:08,577 INFO AddWeight Resolution [bp]: 50000 2021-09-29 05:58:08,600 INFO AddWeight AddWeight successfully finished 2021-09-29 05:58:08,602 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter.hic 2021-09-29 05:58:08,602 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_norm.hic 2021-09-29 05:58:08,602 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/vector.txt 2021-09-29 05:58:08,602 INFO Vector2HiC Threads: 10 2021-09-29 05:58:08,623 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter.hic" "/tmp/tmpj919ct5i/inter.hic" 2021-09-29 05:58:08,997 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-29 05:58:08,997 INFO Vector2HiC Vector: vector c-tale_normalization chr11 5000 BP 2021-09-29 05:58:08,999 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpj919ct5i/inter.hic" "/tmp/tmpj919ct5i/vector.txt" 2021-09-29 05:58:13,893 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-29 05:58:13,893 INFO Vector2HiC Vector: vector c-tale_normalization chr11 10000 BP 2021-09-29 05:58:13,894 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpj919ct5i/inter.hic" "/tmp/tmpj919ct5i/vector.txt" 2021-09-29 05:58:18,583 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-29 05:58:18,583 INFO Vector2HiC Vector: vector c-tale_normalization chr11 20000 BP 2021-09-29 05:58:18,687 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpj919ct5i/inter.hic" "/tmp/tmpj919ct5i/vector.txt" 2021-09-29 05:58:22,844 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-29 05:58:22,844 INFO Vector2HiC Vector: vector c-tale_normalization chr11 25000 BP 2021-09-29 05:58:22,845 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpj919ct5i/inter.hic" "/tmp/tmpj919ct5i/vector.txt" 2021-09-29 05:58:27,082 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-29 05:58:27,082 INFO Vector2HiC Vector: vector c-tale_normalization chr11 50000 BP 2021-09-29 05:58:27,082 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpj919ct5i/inter.hic" "/tmp/tmpj919ct5i/vector.txt" 2021-09-29 05:58:31,362 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-29 05:58:31,362 DEBUG SimpleSubprocess cp "/tmp/tmpj919ct5i/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_norm.hic" 2021-09-29 05:58:31,826 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-29 05:58:31,896 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/merged_nodups.txt" 2021-09-29 05:59:59,328 INFO SimpleSubprocess CopyResult - 0:01:27 2021-09-29 05:59:59,328 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter.pairs.txt" 2021-09-29 06:00:19,956 INFO SimpleSubprocess CopyResult - 0:00:20 2021-09-29 06:00:19,956 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/vector.txt" 2021-09-29 06:00:19,965 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:19,966 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter.hic" 2021-09-29 06:00:23,320 INFO SimpleSubprocess CopyResult - 0:00:03 2021-09-29 06:00:23,320 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter_statistics.txt" 2021-09-29 06:00:23,328 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:23,328 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter_no_balanced_5kb.cool" 2021-09-29 06:00:23,717 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:23,718 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter_5kb.cool" 2021-09-29 06:00:23,930 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:23,931 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter_no_balanced_10kb.cool" 2021-09-29 06:00:24,256 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:24,256 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter_10kb.cool" 2021-09-29 06:00:24,583 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:24,584 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter_no_balanced_20kb.cool" 2021-09-29 06:00:25,132 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:25,133 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter_20kb.cool" 2021-09-29 06:00:25,288 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:25,288 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter_no_balanced_25kb.cool" 2021-09-29 06:00:25,835 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:25,835 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter_25kb.cool" 2021-09-29 06:00:26,154 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:26,155 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter_no_balanced_50kb.cool" 2021-09-29 06:00:26,670 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:26,671 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/inter_50kb.cool" 2021-09-29 06:00:27,051 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-29 06:00:27,176 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8453401-SRR8453402/__temp__" 2021-09-29 06:00:37,283 INFO SimpleSubprocess RemoveTemp - 0:00:10 2021-09-29 06:00:37,284 INFO BenchmarkPipeline 'SRR8453401-SRR8453402' FINISHED, SUMMARY TIME - 9:19:59