2021-09-06 19:49:51,144 INFO BenchmarkPipeline --- START PROCESSING 'SRR6024981-SRR6024982' --- 2021-09-06 19:49:51,145 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024981.sra 2021-09-06 19:49:51,145 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__ 2021-09-06 19:49:51,170 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp8vzdjiey "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024981.sra" 2021-09-06 20:06:44,690 INFO SimpleSubprocess Sra2FastQ - 0:16:53 2021-09-06 20:06:44,704 DEBUG SimpleSubprocess gzip /tmp/tmp8vzdjiey/* 2021-09-06 21:05:35,812 INFO SimpleSubprocess GZipFastQ - 0:58:51 2021-09-06 21:05:35,924 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/fastq"; mv /tmp/tmp8vzdjiey/SRR6024981_2.fastq.gz /tmp/tmp8vzdjiey/SRR6024981_R2.fastq.gz; mv /tmp/tmp8vzdjiey/SRR6024981_1.fastq.gz /tmp/tmp8vzdjiey/SRR6024981_R1.fastq.gz; cp /tmp/tmp8vzdjiey/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/fastq" 2021-09-06 21:05:55,920 INFO SimpleSubprocess CopyFiles - 0:00:19 2021-09-06 21:05:57,248 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024982.sra 2021-09-06 21:05:57,250 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__ 2021-09-06 21:05:57,250 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpx3ydxc6a "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024982.sra" 2021-09-06 21:19:33,666 INFO SimpleSubprocess Sra2FastQ - 0:13:36 2021-09-06 21:19:33,687 DEBUG SimpleSubprocess gzip /tmp/tmpx3ydxc6a/* 2021-09-06 21:48:58,159 INFO SimpleSubprocess GZipFastQ - 0:29:24 2021-09-06 21:48:58,159 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/fastq"; mv /tmp/tmpx3ydxc6a/SRR6024982_2.fastq.gz /tmp/tmpx3ydxc6a/SRR6024982_R2.fastq.gz; mv /tmp/tmpx3ydxc6a/SRR6024982_1.fastq.gz /tmp/tmpx3ydxc6a/SRR6024982_R1.fastq.gz; cp /tmp/tmpx3ydxc6a/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/fastq" 2021-09-06 21:49:04,178 INFO SimpleSubprocess CopyFiles - 0:00:06 2021-09-06 21:49:05,110 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__ 2021-09-06 21:49:05,110 INFO Juicer Genome assembly: mm10 2021-09-06 21:49:05,110 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-06 21:49:05,110 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-06 21:49:05,110 INFO Juicer Enzyme: DpnII 2021-09-06 21:49:05,110 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-06 21:49:05,110 INFO Juicer Threads: 10 2021-09-06 21:49:05,111 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/splits" 2021-09-06 21:49:05,133 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-06 21:49:05,133 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/SRR6024981-SRR6024982/__temp__" 2021-09-07 06:54:56,269 INFO SimpleSubprocess Juicer - 9:05:51 2021-09-07 06:54:56,333 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/SRR6024981-SRR6024982/__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/SRR6024981-SRR6024982/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/splits/SRR6024981_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/splits/SRR6024981_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/splits/SRR6024981.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/splits/SRR6024981.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/splits/SRR6024982_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/splits/SRR6024982_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/splits/SRR6024982.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/splits/SRR6024982.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 [2021-09-07T04:33:40,945] [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 [2021-09-07T05:06:32,167] [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/SRR6024981-SRR6024982/__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 [2021-09-07T06:54:55,480] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__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/SRR6024981-SRR6024982/__temp__/aligned for results 2021-09-07 06:54:56,536 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/merged_nodups.txt 2021-09-07 06:54:56,536 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt 2021-09-07 06:54:56,651 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpb38e9yli/inter.pairs.txt" 2021-09-07 06:55:51,931 INFO SimpleSubprocess MakeInterPairs - 0:00:55 2021-09-07 06:55:51,931 DEBUG SimpleSubprocess cp "/tmp/tmpb38e9yli/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt" 2021-09-07 06:55:53,321 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-07 06:55:53,589 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt 2021-09-07 06:55:53,589 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-07 06:55:53,589 INFO Pairs2Cool Genome assembly: mm10 2021-09-07 06:55:53,589 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-07 06:55:53,589 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-07 06:55:53,615 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/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt" "/tmp/tmpns4_gwtf/inter_no_balanced.cool" 2021-09-07 06:57:21,498 INFO SimpleSubprocess MakeCool - 0:01:27 2021-09-07 06:57:21,498 DEBUG SimpleSubprocess cp "/tmp/tmpns4_gwtf/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-07 06:57:21,530 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 06:57:21,842 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt 2021-09-07 06:57:21,842 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-07 06:57:21,842 INFO Pairs2Cool Genome assembly: mm10 2021-09-07 06:57:21,842 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-07 06:57:21,842 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-07 06:57:21,843 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/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt" "/tmp/tmpshso65k4/inter_no_balanced.cool" 2021-09-07 06:58:38,704 INFO SimpleSubprocess MakeCool - 0:01:16 2021-09-07 06:58:38,704 DEBUG SimpleSubprocess cp "/tmp/tmpshso65k4/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-07 06:58:38,731 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 06:58:38,735 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt 2021-09-07 06:58:38,735 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-07 06:58:38,735 INFO Pairs2Cool Genome assembly: mm10 2021-09-07 06:58:38,735 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-07 06:58:38,735 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-07 06:58:38,735 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/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt" "/tmp/tmp350n7yop/inter_no_balanced.cool" 2021-09-07 06:59:49,791 INFO SimpleSubprocess MakeCool - 0:01:11 2021-09-07 06:59:49,791 DEBUG SimpleSubprocess cp "/tmp/tmp350n7yop/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-07 06:59:49,815 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 06:59:49,818 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt 2021-09-07 06:59:49,818 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-07 06:59:49,818 INFO Pairs2Cool Genome assembly: mm10 2021-09-07 06:59:49,818 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-07 06:59:49,818 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-07 06:59:49,818 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/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt" "/tmp/tmptft2ntzn/inter_no_balanced.cool" 2021-09-07 07:01:00,040 INFO SimpleSubprocess MakeCool - 0:01:10 2021-09-07 07:01:00,041 DEBUG SimpleSubprocess cp "/tmp/tmptft2ntzn/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-07 07:01:00,064 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 07:01:00,067 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt 2021-09-07 07:01:00,068 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-07 07:01:00,068 INFO Pairs2Cool Genome assembly: mm10 2021-09-07 07:01:00,068 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-07 07:01:00,068 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-07 07:01:00,097 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/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt" "/tmp/tmpcjuvr6r2/inter_no_balanced.cool" 2021-09-07 07:02:07,218 INFO SimpleSubprocess MakeCool - 0:01:07 2021-09-07 07:02:07,218 DEBUG SimpleSubprocess cp "/tmp/tmpcjuvr6r2/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-07 07:02:07,237 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 07:02:07,250 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-07 07:02:07,250 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_5kb.cool 2021-09-07 07:02:07,250 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-07 07:02:07,250 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpx4jr2xbk/inter.cool" 2021-09-07 07:02:07,281 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 07:02:07,282 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpx4jr2xbk/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-07 07:02:23,510 INFO SimpleSubprocess NormalizeCool - 0:00:16 2021-09-07 07:02:23,511 DEBUG SimpleSubprocess cp "/tmp/tmpx4jr2xbk/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_5kb.cool" 2021-09-07 07:02:23,543 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 07:02:23,546 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-07 07:02:23,547 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_10kb.cool 2021-09-07 07:02:23,547 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-07 07:02:23,607 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp3y6fl7k5/inter.cool" 2021-09-07 07:02:23,634 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 07:02:23,634 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp3y6fl7k5/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-07 07:02:26,275 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-07 07:02:26,276 DEBUG SimpleSubprocess cp "/tmp/tmp3y6fl7k5/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_10kb.cool" 2021-09-07 07:02:26,303 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 07:02:26,362 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-07 07:02:26,362 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_20kb.cool 2021-09-07 07:02:26,362 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-07 07:02:26,385 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmp_4jyh4wg/inter.cool" 2021-09-07 07:02:26,411 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 07:02:26,411 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp_4jyh4wg/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-07 07:02:28,348 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-07 07:02:28,349 DEBUG SimpleSubprocess cp "/tmp/tmp_4jyh4wg/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_20kb.cool" 2021-09-07 07:02:28,374 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 07:02:28,402 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-07 07:02:28,402 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_25kb.cool 2021-09-07 07:02:28,402 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-07 07:02:28,403 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpvfdnjd9k/inter.cool" 2021-09-07 07:02:28,426 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 07:02:28,426 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpvfdnjd9k/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-07 07:02:33,530 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-09-07 07:02:33,530 DEBUG SimpleSubprocess cp "/tmp/tmpvfdnjd9k/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_25kb.cool" 2021-09-07 07:02:33,554 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 07:02:33,557 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-07 07:02:33,557 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_50kb.cool 2021-09-07 07:02:33,557 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-07 07:02:33,557 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpxis71q76/inter.cool" 2021-09-07 07:02:33,577 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 07:02:33,577 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpxis71q76/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-07 07:02:36,381 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-07 07:02:36,381 DEBUG SimpleSubprocess cp "/tmp/tmpxis71q76/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_50kb.cool" 2021-09-07 07:02:36,399 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 07:02:36,403 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/vector.txt 2021-09-07 07:02:36,410 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-07 07:02:36,454 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_5kb.cool 2021-09-07 07:02:36,454 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/vector.txt 2021-09-07 07:02:36,454 INFO AddWeight Chromosome: chr13 2021-09-07 07:02:36,454 INFO AddWeight Resolution [bp]: 5000 2021-09-07 07:02:37,857 INFO AddWeight AddWeight successfully finished 2021-09-07 07:02:37,857 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_10kb.cool 2021-09-07 07:02:37,857 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/vector.txt 2021-09-07 07:02:37,857 INFO AddWeight Chromosome: chr13 2021-09-07 07:02:37,857 INFO AddWeight Resolution [bp]: 10000 2021-09-07 07:02:37,909 INFO AddWeight AddWeight successfully finished 2021-09-07 07:02:37,909 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_20kb.cool 2021-09-07 07:02:37,910 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/vector.txt 2021-09-07 07:02:37,910 INFO AddWeight Chromosome: chr13 2021-09-07 07:02:37,910 INFO AddWeight Resolution [bp]: 20000 2021-09-07 07:02:37,944 INFO AddWeight AddWeight successfully finished 2021-09-07 07:02:37,944 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_25kb.cool 2021-09-07 07:02:37,944 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/vector.txt 2021-09-07 07:02:37,944 INFO AddWeight Chromosome: chr13 2021-09-07 07:02:37,944 INFO AddWeight Resolution [bp]: 25000 2021-09-07 07:02:37,968 INFO AddWeight AddWeight successfully finished 2021-09-07 07:02:37,968 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_50kb.cool 2021-09-07 07:02:37,968 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/vector.txt 2021-09-07 07:02:37,968 INFO AddWeight Chromosome: chr13 2021-09-07 07:02:37,968 INFO AddWeight Resolution [bp]: 50000 2021-09-07 07:02:37,988 INFO AddWeight AddWeight successfully finished 2021-09-07 07:02:37,990 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter.hic 2021-09-07 07:02:37,990 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_norm.hic 2021-09-07 07:02:37,990 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/vector.txt 2021-09-07 07:02:37,990 INFO Vector2HiC Threads: 10 2021-09-07 07:02:38,030 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter.hic" "/tmp/tmp_1vc1oeg/inter.hic" 2021-09-07 07:02:38,331 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 07:02:38,331 INFO Vector2HiC Vector: vector c-tale_normalization chr13 5000 BP 2021-09-07 07:02:38,332 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp_1vc1oeg/inter.hic" "/tmp/tmp_1vc1oeg/vector.txt" 2021-09-07 07:02:42,875 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-07 07:02:42,875 INFO Vector2HiC Vector: vector c-tale_normalization chr13 10000 BP 2021-09-07 07:02:42,876 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp_1vc1oeg/inter.hic" "/tmp/tmp_1vc1oeg/vector.txt" 2021-09-07 07:02:46,764 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-07 07:02:46,765 INFO Vector2HiC Vector: vector c-tale_normalization chr13 20000 BP 2021-09-07 07:02:46,765 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp_1vc1oeg/inter.hic" "/tmp/tmp_1vc1oeg/vector.txt" 2021-09-07 07:02:50,340 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-07 07:02:50,340 INFO Vector2HiC Vector: vector c-tale_normalization chr13 25000 BP 2021-09-07 07:02:50,341 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp_1vc1oeg/inter.hic" "/tmp/tmp_1vc1oeg/vector.txt" 2021-09-07 07:02:53,973 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-07 07:02:53,974 INFO Vector2HiC Vector: vector c-tale_normalization chr13 50000 BP 2021-09-07 07:02:53,974 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp_1vc1oeg/inter.hic" "/tmp/tmp_1vc1oeg/vector.txt" 2021-09-07 07:02:57,687 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-07 07:02:57,687 DEBUG SimpleSubprocess cp "/tmp/tmp_1vc1oeg/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_norm.hic" 2021-09-07 07:02:58,039 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 07:02:58,093 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/merged_nodups.txt" 2021-09-07 07:03:38,168 INFO SimpleSubprocess CopyResult - 0:00:40 2021-09-07 07:03:38,168 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter.pairs.txt" 2021-09-07 07:03:50,251 INFO SimpleSubprocess CopyResult - 0:00:12 2021-09-07 07:03:50,251 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/vector.txt" 2021-09-07 07:03:50,260 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:50,260 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter.hic" 2021-09-07 07:03:53,118 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-07 07:03:53,119 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter_statistics.txt" 2021-09-07 07:03:53,126 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:53,126 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter_no_balanced_5kb.cool" 2021-09-07 07:03:53,329 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:53,329 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter_5kb.cool" 2021-09-07 07:03:53,560 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:53,560 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter_no_balanced_10kb.cool" 2021-09-07 07:03:53,743 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:53,744 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter_10kb.cool" 2021-09-07 07:03:53,867 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:53,867 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter_no_balanced_20kb.cool" 2021-09-07 07:03:53,981 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:53,981 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter_20kb.cool" 2021-09-07 07:03:54,080 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:54,080 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter_no_balanced_25kb.cool" 2021-09-07 07:03:54,215 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:54,216 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter_25kb.cool" 2021-09-07 07:03:54,343 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:54,343 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter_no_balanced_50kb.cool" 2021-09-07 07:03:54,435 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:54,435 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/inter_50kb.cool" 2021-09-07 07:03:54,493 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 07:03:54,639 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__" 2021-09-07 07:04:10,724 INFO SimpleSubprocess RemoveTemp - 0:00:16 2021-09-07 07:04:10,725 INFO BenchmarkPipeline 'SRR6024981-SRR6024982' FINISHED, SUMMARY TIME - 11:14:19 2021-09-10 13:00:59,213 INFO BenchmarkPipeline --- START PROCESSING 'SRR6024981-SRR6024982' --- 2021-09-10 13:00:59,244 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024981-SRR6024982/__temp__" 2021-09-10 13:00:59,253 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-10 13:00:59,253 INFO BenchmarkPipeline 'SRR6024981-SRR6024982' FINISHED, SUMMARY TIME - 0:00:00