2021-09-06 08:02:19,036 INFO BenchmarkPipeline --- START PROCESSING 'SRR6024979-SRR6024980' --- 2021-09-06 08:02:19,036 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024979.sra 2021-09-06 08:02:19,037 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__ 2021-09-06 08:02:19,037 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpkxktmd_l "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024979.sra" 2021-09-06 08:19:07,894 INFO SimpleSubprocess Sra2FastQ - 0:16:48 2021-09-06 08:19:07,919 DEBUG SimpleSubprocess gzip /tmp/tmpkxktmd_l/* 2021-09-06 09:21:11,468 INFO SimpleSubprocess GZipFastQ - 1:02:03 2021-09-06 09:21:11,682 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/fastq"; mv /tmp/tmpkxktmd_l/SRR6024979_1.fastq.gz /tmp/tmpkxktmd_l/SRR6024979_R1.fastq.gz; mv /tmp/tmpkxktmd_l/SRR6024979_2.fastq.gz /tmp/tmpkxktmd_l/SRR6024979_R2.fastq.gz; cp /tmp/tmpkxktmd_l/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/fastq" 2021-09-06 09:21:39,668 INFO SimpleSubprocess CopyFiles - 0:00:27 2021-09-06 09:21:41,036 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024980.sra 2021-09-06 09:21:41,036 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__ 2021-09-06 09:21:41,142 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpt1vjj3k8 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024980.sra" 2021-09-06 09:36:02,203 INFO SimpleSubprocess Sra2FastQ - 0:14:21 2021-09-06 09:36:02,224 DEBUG SimpleSubprocess gzip /tmp/tmpt1vjj3k8/* 2021-09-06 10:07:58,050 INFO SimpleSubprocess GZipFastQ - 0:31:55 2021-09-06 10:07:58,082 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/fastq"; mv /tmp/tmpt1vjj3k8/SRR6024980_1.fastq.gz /tmp/tmpt1vjj3k8/SRR6024980_R1.fastq.gz; mv /tmp/tmpt1vjj3k8/SRR6024980_2.fastq.gz /tmp/tmpt1vjj3k8/SRR6024980_R2.fastq.gz; cp /tmp/tmpt1vjj3k8/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/fastq" 2021-09-06 10:08:04,128 INFO SimpleSubprocess CopyFiles - 0:00:06 2021-09-06 10:08:05,248 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__ 2021-09-06 10:08:05,248 INFO Juicer Genome assembly: mm10 2021-09-06 10:08:05,248 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-06 10:08:05,248 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-06 10:08:05,249 INFO Juicer Enzyme: DpnII 2021-09-06 10:08:05,249 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-06 10:08:05,249 INFO Juicer Threads: 10 2021-09-06 10:08:05,249 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/splits" 2021-09-06 10:08:05,335 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-06 10:08:05,335 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/SRR6024979-SRR6024980/__temp__" 2021-09-06 19:40:31,306 INFO SimpleSubprocess Juicer - 9:32:25 2021-09-06 19:40:31,375 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/SRR6024979-SRR6024980/__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/SRR6024979-SRR6024980/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/splits/SRR6024979_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/splits/SRR6024979_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/splits/SRR6024979.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/splits/SRR6024979.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/splits/SRR6024980_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/splits/SRR6024980_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/splits/SRR6024980.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/splits/SRR6024980.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 [2021-09-06T17:41:21,236] [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 [2021-09-06T18:11:08,378] [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/SRR6024979-SRR6024980/__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 [2021-09-06T19:40:30,418] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__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/SRR6024979-SRR6024980/__temp__/aligned for results 2021-09-06 19:40:31,603 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/merged_nodups.txt 2021-09-06 19:40:31,603 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt 2021-09-06 19:40:31,683 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpex_8r4xf/inter.pairs.txt" 2021-09-06 19:41:26,544 INFO SimpleSubprocess MakeInterPairs - 0:00:54 2021-09-06 19:41:26,544 DEBUG SimpleSubprocess cp "/tmp/tmpex_8r4xf/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt" 2021-09-06 19:41:27,972 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-06 19:41:28,281 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt 2021-09-06 19:41:28,282 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-06 19:41:28,282 INFO Pairs2Cool Genome assembly: mm10 2021-09-06 19:41:28,282 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-06 19:41:28,282 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-06 19:41:28,298 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/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt" "/tmp/tmpph1n1r3s/inter_no_balanced.cool" 2021-09-06 19:43:00,186 INFO SimpleSubprocess MakeCool - 0:01:31 2021-09-06 19:43:00,187 DEBUG SimpleSubprocess cp "/tmp/tmpph1n1r3s/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-06 19:43:00,222 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-06 19:43:00,264 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt 2021-09-06 19:43:00,264 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-06 19:43:00,264 INFO Pairs2Cool Genome assembly: mm10 2021-09-06 19:43:00,264 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-06 19:43:00,264 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-06 19:43:00,279 DEBUG SimpleSubprocess cooler cload pairs -c1 1 -p1 2 -c2 3 -p2 4 --assembly mm10 "/Data/DataBases/mm10/mm10_canonic.chrom.sizes":10000 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt" "/tmp/tmp0ado3afg/inter_no_balanced.cool" 2021-09-06 19:44:21,311 INFO SimpleSubprocess MakeCool - 0:01:21 2021-09-06 19:44:21,312 DEBUG SimpleSubprocess cp "/tmp/tmp0ado3afg/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-06 19:44:21,342 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-06 19:44:21,359 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt 2021-09-06 19:44:21,359 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-06 19:44:21,359 INFO Pairs2Cool Genome assembly: mm10 2021-09-06 19:44:21,359 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-06 19:44:21,359 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-06 19:44:21,390 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/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt" "/tmp/tmpg7r0ttye/inter_no_balanced.cool" 2021-09-06 19:45:38,567 INFO SimpleSubprocess MakeCool - 0:01:17 2021-09-06 19:45:38,567 DEBUG SimpleSubprocess cp "/tmp/tmpg7r0ttye/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-06 19:45:38,596 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-06 19:45:38,600 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt 2021-09-06 19:45:38,600 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-06 19:45:38,600 INFO Pairs2Cool Genome assembly: mm10 2021-09-06 19:45:38,600 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-06 19:45:38,600 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-06 19:45:38,619 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/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt" "/tmp/tmp0mesv5ne/inter_no_balanced.cool" 2021-09-06 19:46:53,375 INFO SimpleSubprocess MakeCool - 0:01:14 2021-09-06 19:46:53,375 DEBUG SimpleSubprocess cp "/tmp/tmp0mesv5ne/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-06 19:46:53,401 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-06 19:46:53,462 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt 2021-09-06 19:46:53,462 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-06 19:46:53,462 INFO Pairs2Cool Genome assembly: mm10 2021-09-06 19:46:53,462 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-06 19:46:53,462 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-06 19:46:53,462 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/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt" "/tmp/tmpc64s0u9i/inter_no_balanced.cool" 2021-09-06 19:48:04,279 INFO SimpleSubprocess MakeCool - 0:01:10 2021-09-06 19:48:04,279 DEBUG SimpleSubprocess cp "/tmp/tmpc64s0u9i/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-06 19:48:04,300 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-06 19:48:04,369 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-06 19:48:04,369 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_5kb.cool 2021-09-06 19:48:04,369 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-06 19:48:04,380 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp6a8_04pv/inter.cool" 2021-09-06 19:48:04,416 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-06 19:48:04,416 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp6a8_04pv/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-06 19:48:09,363 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-09-06 19:48:09,363 DEBUG SimpleSubprocess cp "/tmp/tmp6a8_04pv/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_5kb.cool" 2021-09-06 19:48:09,430 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-06 19:48:09,434 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-06 19:48:09,434 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_10kb.cool 2021-09-06 19:48:09,434 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-06 19:48:09,477 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp3oxq1rv8/inter.cool" 2021-09-06 19:48:09,507 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-06 19:48:09,507 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp3oxq1rv8/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-06 19:48:12,031 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-06 19:48:12,031 DEBUG SimpleSubprocess cp "/tmp/tmp3oxq1rv8/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_10kb.cool" 2021-09-06 19:48:12,061 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-06 19:48:12,065 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-06 19:48:12,065 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_20kb.cool 2021-09-06 19:48:12,065 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-06 19:48:12,065 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpa1ghystz/inter.cool" 2021-09-06 19:48:12,102 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-06 19:48:12,102 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpa1ghystz/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-06 19:48:13,804 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-06 19:48:13,805 DEBUG SimpleSubprocess cp "/tmp/tmpa1ghystz/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_20kb.cool" 2021-09-06 19:48:13,832 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-06 19:48:13,835 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-06 19:48:13,835 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_25kb.cool 2021-09-06 19:48:13,835 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-06 19:48:13,852 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpkq4d1oy_/inter.cool" 2021-09-06 19:48:13,877 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-06 19:48:13,877 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpkq4d1oy_/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-06 19:48:15,404 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-06 19:48:15,404 DEBUG SimpleSubprocess cp "/tmp/tmpkq4d1oy_/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_25kb.cool" 2021-09-06 19:48:15,430 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-06 19:48:15,433 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-06 19:48:15,433 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_50kb.cool 2021-09-06 19:48:15,433 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-06 19:48:15,452 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpaapvjf5n/inter.cool" 2021-09-06 19:48:15,472 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-06 19:48:15,473 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpaapvjf5n/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-06 19:48:16,612 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-06 19:48:16,613 DEBUG SimpleSubprocess cp "/tmp/tmpaapvjf5n/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_50kb.cool" 2021-09-06 19:48:16,634 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-06 19:48:16,650 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/vector.txt 2021-09-06 19:48:16,655 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-06 19:48:16,656 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_5kb.cool 2021-09-06 19:48:16,656 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/vector.txt 2021-09-06 19:48:16,656 INFO AddWeight Chromosome: chr13 2021-09-06 19:48:16,656 INFO AddWeight Resolution [bp]: 5000 2021-09-06 19:48:18,157 INFO AddWeight AddWeight successfully finished 2021-09-06 19:48:18,158 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_10kb.cool 2021-09-06 19:48:18,158 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/vector.txt 2021-09-06 19:48:18,158 INFO AddWeight Chromosome: chr13 2021-09-06 19:48:18,158 INFO AddWeight Resolution [bp]: 10000 2021-09-06 19:48:18,210 INFO AddWeight AddWeight successfully finished 2021-09-06 19:48:18,210 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_20kb.cool 2021-09-06 19:48:18,210 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/vector.txt 2021-09-06 19:48:18,210 INFO AddWeight Chromosome: chr13 2021-09-06 19:48:18,210 INFO AddWeight Resolution [bp]: 20000 2021-09-06 19:48:18,241 INFO AddWeight AddWeight successfully finished 2021-09-06 19:48:18,241 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_25kb.cool 2021-09-06 19:48:18,241 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/vector.txt 2021-09-06 19:48:18,241 INFO AddWeight Chromosome: chr13 2021-09-06 19:48:18,241 INFO AddWeight Resolution [bp]: 25000 2021-09-06 19:48:18,268 INFO AddWeight AddWeight successfully finished 2021-09-06 19:48:18,268 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_50kb.cool 2021-09-06 19:48:18,268 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/vector.txt 2021-09-06 19:48:18,268 INFO AddWeight Chromosome: chr13 2021-09-06 19:48:18,268 INFO AddWeight Resolution [bp]: 50000 2021-09-06 19:48:18,289 INFO AddWeight AddWeight successfully finished 2021-09-06 19:48:18,291 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.hic 2021-09-06 19:48:18,291 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_norm.hic 2021-09-06 19:48:18,291 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/vector.txt 2021-09-06 19:48:18,291 INFO Vector2HiC Threads: 10 2021-09-06 19:48:18,312 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.hic" "/tmp/tmpbk84vvb6/inter.hic" 2021-09-06 19:48:18,635 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-06 19:48:18,636 INFO Vector2HiC Vector: vector c-tale_normalization chr13 5000 BP 2021-09-06 19:48:18,637 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpbk84vvb6/inter.hic" "/tmp/tmpbk84vvb6/vector.txt" 2021-09-06 19:48:22,942 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-06 19:48:22,942 INFO Vector2HiC Vector: vector c-tale_normalization chr13 10000 BP 2021-09-06 19:48:22,943 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpbk84vvb6/inter.hic" "/tmp/tmpbk84vvb6/vector.txt" 2021-09-06 19:48:26,849 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-06 19:48:26,849 INFO Vector2HiC Vector: vector c-tale_normalization chr13 20000 BP 2021-09-06 19:48:26,850 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpbk84vvb6/inter.hic" "/tmp/tmpbk84vvb6/vector.txt" 2021-09-06 19:48:31,875 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-09-06 19:48:31,876 INFO Vector2HiC Vector: vector c-tale_normalization chr13 25000 BP 2021-09-06 19:48:31,950 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpbk84vvb6/inter.hic" "/tmp/tmpbk84vvb6/vector.txt" 2021-09-06 19:48:35,739 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-06 19:48:35,739 INFO Vector2HiC Vector: vector c-tale_normalization chr13 50000 BP 2021-09-06 19:48:35,739 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpbk84vvb6/inter.hic" "/tmp/tmpbk84vvb6/vector.txt" 2021-09-06 19:48:39,432 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-06 19:48:39,433 DEBUG SimpleSubprocess cp "/tmp/tmpbk84vvb6/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_norm.hic" 2021-09-06 19:48:39,794 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-06 19:48:39,907 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/merged_nodups.txt" 2021-09-06 19:49:18,723 INFO SimpleSubprocess CopyResult - 0:00:38 2021-09-06 19:49:18,724 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter.pairs.txt" 2021-09-06 19:49:30,892 INFO SimpleSubprocess CopyResult - 0:00:12 2021-09-06 19:49:30,892 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/vector.txt" 2021-09-06 19:49:30,901 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:30,901 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter.hic" 2021-09-06 19:49:33,736 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-06 19:49:33,736 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter_statistics.txt" 2021-09-06 19:49:33,743 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:33,744 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter_no_balanced_5kb.cool" 2021-09-06 19:49:33,980 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:33,980 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter_5kb.cool" 2021-09-06 19:49:34,228 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:34,228 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter_no_balanced_10kb.cool" 2021-09-06 19:49:34,411 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:34,412 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter_10kb.cool" 2021-09-06 19:49:34,583 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:34,583 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter_no_balanced_20kb.cool" 2021-09-06 19:49:34,728 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:34,728 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter_20kb.cool" 2021-09-06 19:49:34,868 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:34,868 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter_no_balanced_25kb.cool" 2021-09-06 19:49:35,047 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:35,048 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter_25kb.cool" 2021-09-06 19:49:35,167 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:35,168 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter_no_balanced_50kb.cool" 2021-09-06 19:49:35,315 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:35,316 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/inter_50kb.cool" 2021-09-06 19:49:35,463 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-06 19:49:35,470 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__" 2021-09-06 19:49:50,700 INFO SimpleSubprocess RemoveTemp - 0:00:15 2021-09-06 19:49:50,700 INFO BenchmarkPipeline 'SRR6024979-SRR6024980' FINISHED, SUMMARY TIME - 11:47:31 2021-09-10 13:00:59,191 INFO BenchmarkPipeline --- START PROCESSING 'SRR6024979-SRR6024980' --- 2021-09-10 13:00:59,202 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024979-SRR6024980/__temp__" 2021-09-10 13:00:59,212 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-10 13:00:59,212 INFO BenchmarkPipeline 'SRR6024979-SRR6024980' FINISHED, SUMMARY TIME - 0:00:00