2021-09-22 16:57:37,006 INFO BenchmarkPipeline --- START PROCESSING 'SRR7500317' --- 2021-09-22 16:57:37,006 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500317.sra 2021-09-22 16:57:37,006 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__ 2021-09-22 16:57:37,006 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmph_5bik1x "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500317.sra" 2021-09-22 17:17:54,515 INFO SimpleSubprocess Sra2FastQ - 0:20:17 2021-09-22 17:17:54,577 DEBUG SimpleSubprocess gzip /tmp/tmph_5bik1x/* 2021-09-22 18:11:45,885 INFO SimpleSubprocess GZipFastQ - 0:53:51 2021-09-22 18:11:45,886 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/fastq"; mv /tmp/tmph_5bik1x/SRR7500317_2.fastq.gz /tmp/tmph_5bik1x/SRR7500317_R2.fastq.gz; mv /tmp/tmph_5bik1x/SRR7500317_1.fastq.gz /tmp/tmph_5bik1x/SRR7500317_R1.fastq.gz; cp /tmp/tmph_5bik1x/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/fastq" 2021-09-22 18:12:17,026 INFO SimpleSubprocess CopyFiles - 0:00:31 2021-09-22 18:12:18,662 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__ 2021-09-22 18:12:18,662 INFO Juicer Genome assembly: mm10 2021-09-22 18:12:18,662 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-22 18:12:18,662 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 18:12:18,662 INFO Juicer Enzyme: DpnII 2021-09-22 18:12:18,662 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-22 18:12:18,662 INFO Juicer Threads: 10 2021-09-22 18:12:18,662 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/HIC_tmp" 2021-09-22 18:12:18,670 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-22 18:12:18,670 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/SRR7500317/__temp__" 2021-09-22 23:48:55,505 INFO SimpleSubprocess Juicer - 5:36:36 2021-09-22 23:48:55,519 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/SRR7500317/__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/SRR7500317/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/splits/SRR7500317_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/splits/SRR7500317_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/splits/SRR7500317.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/splits/SRR7500317.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 [2021-09-22T22:21:33,569] [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 [2021-09-22T23:08:18,679] [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/SRR7500317/__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 [2021-09-22T23:48:55,135] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__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/SRR7500317/__temp__/aligned for results 2021-09-22 23:48:55,557 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/merged_nodups.txt 2021-09-22 23:48:55,558 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter.pairs.txt 2021-09-22 23:48:55,558 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpukm4ksyn/inter.pairs.txt" 2021-09-22 23:49:38,357 INFO SimpleSubprocess MakeInterPairs - 0:00:42 2021-09-22 23:49:38,357 DEBUG SimpleSubprocess cp "/tmp/tmpukm4ksyn/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter.pairs.txt" 2021-09-22 23:49:39,541 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-22 23:49:39,704 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter.pairs.txt 2021-09-22 23:49:39,704 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-22 23:49:39,704 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 23:49:39,704 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 23:49:39,704 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-22 23:49:39,705 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/SRR7500317/__temp__/aligned/inter.pairs.txt" "/tmp/tmp5n44lojz/inter_no_balanced.cool" 2021-09-22 23:50:49,060 INFO SimpleSubprocess MakeCool - 0:01:09 2021-09-22 23:50:49,060 DEBUG SimpleSubprocess cp "/tmp/tmp5n44lojz/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-22 23:50:49,125 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 23:50:49,129 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter.pairs.txt 2021-09-22 23:50:49,129 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-22 23:50:49,129 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 23:50:49,129 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 23:50:49,129 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-22 23:50:49,129 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/SRR7500317/__temp__/aligned/inter.pairs.txt" "/tmp/tmpr_ccelsq/inter_no_balanced.cool" 2021-09-22 23:51:50,453 INFO SimpleSubprocess MakeCool - 0:01:01 2021-09-22 23:51:50,453 DEBUG SimpleSubprocess cp "/tmp/tmpr_ccelsq/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-22 23:51:50,477 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 23:51:50,480 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter.pairs.txt 2021-09-22 23:51:50,480 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-22 23:51:50,480 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 23:51:50,480 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 23:51:50,480 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-22 23:51:50,480 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/SRR7500317/__temp__/aligned/inter.pairs.txt" "/tmp/tmp5kbegeci/inter_no_balanced.cool" 2021-09-22 23:52:47,640 INFO SimpleSubprocess MakeCool - 0:00:57 2021-09-22 23:52:47,641 DEBUG SimpleSubprocess cp "/tmp/tmp5kbegeci/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-22 23:52:47,661 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 23:52:47,664 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter.pairs.txt 2021-09-22 23:52:47,664 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-22 23:52:47,664 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 23:52:47,664 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 23:52:47,664 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-22 23:52:47,664 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/SRR7500317/__temp__/aligned/inter.pairs.txt" "/tmp/tmpc0w5fk86/inter_no_balanced.cool" 2021-09-22 23:53:43,574 INFO SimpleSubprocess MakeCool - 0:00:55 2021-09-22 23:53:43,575 DEBUG SimpleSubprocess cp "/tmp/tmpc0w5fk86/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-22 23:53:43,594 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 23:53:43,596 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter.pairs.txt 2021-09-22 23:53:43,597 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-22 23:53:43,597 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 23:53:43,597 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 23:53:43,597 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-22 23:53:43,597 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/SRR7500317/__temp__/aligned/inter.pairs.txt" "/tmp/tmp874hglzc/inter_no_balanced.cool" 2021-09-22 23:54:37,261 INFO SimpleSubprocess MakeCool - 0:00:53 2021-09-22 23:54:37,262 DEBUG SimpleSubprocess cp "/tmp/tmp874hglzc/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-22 23:54:37,278 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 23:54:37,451 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-22 23:54:37,451 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_5kb.cool 2021-09-22 23:54:37,451 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-22 23:54:37,451 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp3intou3_/inter.cool" 2021-09-22 23:54:37,477 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 23:54:37,477 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp3intou3_/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-22 23:54:59,812 INFO SimpleSubprocess NormalizeCool - 0:00:22 2021-09-22 23:54:59,812 DEBUG SimpleSubprocess cp "/tmp/tmp3intou3_/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_5kb.cool" 2021-09-22 23:54:59,838 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 23:54:59,841 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-22 23:54:59,841 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_10kb.cool 2021-09-22 23:54:59,841 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-22 23:54:59,841 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp6lej5qgt/inter.cool" 2021-09-22 23:54:59,863 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 23:54:59,863 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp6lej5qgt/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-22 23:55:03,732 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-09-22 23:55:03,732 DEBUG SimpleSubprocess cp "/tmp/tmp6lej5qgt/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_10kb.cool" 2021-09-22 23:55:03,754 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 23:55:03,757 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-22 23:55:03,757 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_20kb.cool 2021-09-22 23:55:03,757 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-22 23:55:03,757 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmppn3i4u19/inter.cool" 2021-09-22 23:55:03,776 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 23:55:03,776 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmppn3i4u19/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-22 23:55:06,604 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-22 23:55:06,605 DEBUG SimpleSubprocess cp "/tmp/tmppn3i4u19/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_20kb.cool" 2021-09-22 23:55:06,624 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 23:55:06,626 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-22 23:55:06,626 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_25kb.cool 2021-09-22 23:55:06,626 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-22 23:55:06,627 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmp3oprtr04/inter.cool" 2021-09-22 23:55:06,645 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 23:55:06,645 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp3oprtr04/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-22 23:55:09,249 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-22 23:55:09,249 DEBUG SimpleSubprocess cp "/tmp/tmp3oprtr04/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_25kb.cool" 2021-09-22 23:55:09,267 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 23:55:09,291 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-22 23:55:09,292 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_50kb.cool 2021-09-22 23:55:09,292 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-09-22 23:55:09,292 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp0d0z927l/inter.cool" 2021-09-22 23:55:09,308 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 23:55:09,308 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp0d0z927l/inter.cool" "chr1:70,945,000-81,015,000" 2021-09-22 23:55:11,173 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-22 23:55:11,173 DEBUG SimpleSubprocess cp "/tmp/tmp0d0z927l/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_50kb.cool" 2021-09-22 23:55:11,191 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 23:55:11,217 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/vector.txt 2021-09-22 23:55:11,224 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-22 23:55:11,224 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_5kb.cool 2021-09-22 23:55:11,224 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/vector.txt 2021-09-22 23:55:11,225 INFO AddWeight Chromosome: chr1 2021-09-22 23:55:11,225 INFO AddWeight Resolution [bp]: 5000 2021-09-22 23:55:11,369 INFO AddWeight AddWeight successfully finished 2021-09-22 23:55:11,370 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_10kb.cool 2021-09-22 23:55:11,370 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/vector.txt 2021-09-22 23:55:11,370 INFO AddWeight Chromosome: chr1 2021-09-22 23:55:11,370 INFO AddWeight Resolution [bp]: 10000 2021-09-22 23:55:11,437 INFO AddWeight AddWeight successfully finished 2021-09-22 23:55:11,437 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_20kb.cool 2021-09-22 23:55:11,437 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/vector.txt 2021-09-22 23:55:11,437 INFO AddWeight Chromosome: chr1 2021-09-22 23:55:11,437 INFO AddWeight Resolution [bp]: 20000 2021-09-22 23:55:11,478 INFO AddWeight AddWeight successfully finished 2021-09-22 23:55:11,478 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_25kb.cool 2021-09-22 23:55:11,478 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/vector.txt 2021-09-22 23:55:11,478 INFO AddWeight Chromosome: chr1 2021-09-22 23:55:11,478 INFO AddWeight Resolution [bp]: 25000 2021-09-22 23:55:11,514 INFO AddWeight AddWeight successfully finished 2021-09-22 23:55:11,514 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_50kb.cool 2021-09-22 23:55:11,514 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/vector.txt 2021-09-22 23:55:11,514 INFO AddWeight Chromosome: chr1 2021-09-22 23:55:11,514 INFO AddWeight Resolution [bp]: 50000 2021-09-22 23:55:11,539 INFO AddWeight AddWeight successfully finished 2021-09-22 23:55:11,541 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter.hic 2021-09-22 23:55:11,541 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_norm.hic 2021-09-22 23:55:11,541 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/vector.txt 2021-09-22 23:55:11,541 INFO Vector2HiC Threads: 10 2021-09-22 23:55:11,618 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter.hic" "/tmp/tmpkqsxszu3/inter.hic" 2021-09-22 23:55:11,870 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 23:55:11,871 INFO Vector2HiC Vector: vector c-tale_normalization chr1 5000 BP 2021-09-22 23:55:11,872 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkqsxszu3/inter.hic" "/tmp/tmpkqsxszu3/vector.txt" 2021-09-22 23:55:16,605 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-22 23:55:16,605 INFO Vector2HiC Vector: vector c-tale_normalization chr1 10000 BP 2021-09-22 23:55:16,606 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkqsxszu3/inter.hic" "/tmp/tmpkqsxszu3/vector.txt" 2021-09-22 23:55:20,500 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-22 23:55:20,500 INFO Vector2HiC Vector: vector c-tale_normalization chr1 20000 BP 2021-09-22 23:55:20,501 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkqsxszu3/inter.hic" "/tmp/tmpkqsxszu3/vector.txt" 2021-09-22 23:55:24,247 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-22 23:55:24,247 INFO Vector2HiC Vector: vector c-tale_normalization chr1 25000 BP 2021-09-22 23:55:24,248 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkqsxszu3/inter.hic" "/tmp/tmpkqsxszu3/vector.txt" 2021-09-22 23:55:28,077 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-22 23:55:28,078 INFO Vector2HiC Vector: vector c-tale_normalization chr1 50000 BP 2021-09-22 23:55:28,078 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkqsxszu3/inter.hic" "/tmp/tmpkqsxszu3/vector.txt" 2021-09-22 23:55:31,869 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-22 23:55:31,870 DEBUG SimpleSubprocess cp "/tmp/tmpkqsxszu3/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_norm.hic" 2021-09-22 23:55:32,174 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 23:55:32,224 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/merged_nodups.txt" 2021-09-22 23:55:44,191 INFO SimpleSubprocess CopyResult - 0:00:11 2021-09-22 23:55:44,191 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter.pairs.txt" 2021-09-22 23:55:52,190 INFO SimpleSubprocess CopyResult - 0:00:07 2021-09-22 23:55:52,191 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/vector.txt" 2021-09-22 23:55:52,233 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:52,233 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter.hic" 2021-09-22 23:55:54,415 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-22 23:55:54,416 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter_statistics.txt" 2021-09-22 23:55:54,423 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:54,424 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter_no_balanced_5kb.cool" 2021-09-22 23:55:54,586 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:54,587 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter_5kb.cool" 2021-09-22 23:55:54,750 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:54,751 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter_no_balanced_10kb.cool" 2021-09-22 23:55:54,868 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:54,868 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter_10kb.cool" 2021-09-22 23:55:54,984 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:54,984 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter_no_balanced_20kb.cool" 2021-09-22 23:55:55,083 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:55,083 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter_20kb.cool" 2021-09-22 23:55:55,183 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:55,183 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter_no_balanced_25kb.cool" 2021-09-22 23:55:55,282 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:55,283 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter_25kb.cool" 2021-09-22 23:55:55,368 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:55,368 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter_no_balanced_50kb.cool" 2021-09-22 23:55:55,436 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:55,436 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/inter_50kb.cool" 2021-09-22 23:55:55,518 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 23:55:55,742 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500317/__temp__" 2021-09-22 23:56:03,227 INFO SimpleSubprocess RemoveTemp - 0:00:07 2021-09-22 23:56:03,227 INFO BenchmarkPipeline 'SRR7500317' FINISHED, SUMMARY TIME - 6:58:26