2021-08-25 13:48:20,351 INFO BenchmarkPipeline --- START PROCESSING 'SRR7500315' --- 2021-08-25 13:48:20,351 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500315.sra 2021-08-25 13:48:20,351 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__ 2021-08-25 13:48:20,352 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpolxza5m8 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7500315.sra" 2021-08-25 14:23:28,927 INFO SimpleSubprocess Sra2FastQ - 0:35:08 2021-08-25 14:23:28,948 DEBUG SimpleSubprocess gzip /tmp/tmpolxza5m8/* 2021-08-25 16:57:20,289 INFO SimpleSubprocess GZipFastQ - 2:33:51 2021-08-25 16:57:20,359 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/fastq"; mv /tmp/tmpolxza5m8/SRR7500315_1.fastq.gz /tmp/tmpolxza5m8/SRR7500315_R1.fastq.gz; mv /tmp/tmpolxza5m8/SRR7500315_2.fastq.gz /tmp/tmpolxza5m8/SRR7500315_R2.fastq.gz; cp /tmp/tmpolxza5m8/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/fastq" 2021-08-25 17:02:04,716 INFO SimpleSubprocess CopyFiles - 0:04:44 2021-08-25 17:02:06,790 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__ 2021-08-25 17:02:06,790 INFO Juicer Genome assembly: mm10 2021-08-25 17:02:06,790 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-25 17:02:06,790 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-25 17:02:06,790 INFO Juicer Enzyme: DpnII 2021-08-25 17:02:06,790 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-25 17:02:06,790 INFO Juicer Threads: 10 2021-08-25 17:02:06,790 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/SRR7500315/__temp__" 2021-08-25 19:33:28,261 INFO BenchmarkPipeline --- START PROCESSING 'SRR7500315' --- 2021-08-25 19:33:28,273 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__ 2021-08-25 19:33:28,273 INFO Juicer Genome assembly: mm10 2021-08-25 19:33:28,274 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-08-25 19:33:28,274 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-25 19:33:28,274 INFO Juicer Enzyme: DpnII 2021-08-25 19:33:28,274 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-08-25 19:33:28,274 INFO Juicer Threads: 10 2021-08-25 19:33:28,274 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/SRR7500315/__temp__" 2021-08-26 04:40:56,246 INFO SimpleSubprocess Juicer - 9:07:27 2021-08-26 04:40:56,260 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/SRR7500315/__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/SRR7500315/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/splits/SRR7500315_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/splits/SRR7500315_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/splits/SRR7500315.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/splits/SRR7500315.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 [2021-08-26T02:38:57,736] [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 [2021-08-26T03:15:40,759] [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/SRR7500315/__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 [2021-08-26T04:40:55,846] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__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/SRR7500315/__temp__/aligned for results 2021-08-26 04:40:56,295 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/merged_nodups.txt 2021-08-26 04:40:56,295 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter.pairs.txt 2021-08-26 04:40:56,296 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpbn7_qmsu/inter.pairs.txt" 2021-08-26 04:42:01,938 INFO SimpleSubprocess MakeInterPairs - 0:01:05 2021-08-26 04:42:01,938 DEBUG SimpleSubprocess cp "/tmp/tmpbn7_qmsu/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter.pairs.txt" 2021-08-26 04:42:03,485 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-08-26 04:42:03,703 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter.pairs.txt 2021-08-26 04:42:03,703 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-26 04:42:03,703 INFO Pairs2Cool Genome assembly: mm10 2021-08-26 04:42:03,703 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 04:42:03,703 INFO Pairs2Cool Resolution [bp]: 5000 2021-08-26 04:42:03,704 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/SRR7500315/__temp__/aligned/inter.pairs.txt" "/tmp/tmpv6h6y467/inter_no_balanced.cool" 2021-08-26 04:43:29,565 INFO SimpleSubprocess MakeCool - 0:01:25 2021-08-26 04:43:29,565 DEBUG SimpleSubprocess cp "/tmp/tmpv6h6y467/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-08-26 04:43:29,597 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 04:43:29,601 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter.pairs.txt 2021-08-26 04:43:29,601 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-26 04:43:29,601 INFO Pairs2Cool Genome assembly: mm10 2021-08-26 04:43:29,601 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 04:43:29,601 INFO Pairs2Cool Resolution [bp]: 10000 2021-08-26 04:43:29,601 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/SRR7500315/__temp__/aligned/inter.pairs.txt" "/tmp/tmp143_th5i/inter_no_balanced.cool" 2021-08-26 04:44:47,367 INFO SimpleSubprocess MakeCool - 0:01:17 2021-08-26 04:44:47,368 DEBUG SimpleSubprocess cp "/tmp/tmp143_th5i/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-08-26 04:44:47,391 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 04:44:47,394 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter.pairs.txt 2021-08-26 04:44:47,394 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-26 04:44:47,395 INFO Pairs2Cool Genome assembly: mm10 2021-08-26 04:44:47,395 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 04:44:47,395 INFO Pairs2Cool Resolution [bp]: 20000 2021-08-26 04:44:47,395 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/SRR7500315/__temp__/aligned/inter.pairs.txt" "/tmp/tmpzu4_nlld/inter_no_balanced.cool" 2021-08-26 04:46:02,810 INFO SimpleSubprocess MakeCool - 0:01:15 2021-08-26 04:46:02,810 DEBUG SimpleSubprocess cp "/tmp/tmpzu4_nlld/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-08-26 04:46:02,832 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 04:46:02,834 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter.pairs.txt 2021-08-26 04:46:02,835 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-26 04:46:02,835 INFO Pairs2Cool Genome assembly: mm10 2021-08-26 04:46:02,835 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 04:46:02,835 INFO Pairs2Cool Resolution [bp]: 25000 2021-08-26 04:46:02,835 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/SRR7500315/__temp__/aligned/inter.pairs.txt" "/tmp/tmp9420epb_/inter_no_balanced.cool" 2021-08-26 04:47:15,594 INFO SimpleSubprocess MakeCool - 0:01:12 2021-08-26 04:47:15,594 DEBUG SimpleSubprocess cp "/tmp/tmp9420epb_/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-08-26 04:47:15,615 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 04:47:15,617 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter.pairs.txt 2021-08-26 04:47:15,617 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-26 04:47:15,617 INFO Pairs2Cool Genome assembly: mm10 2021-08-26 04:47:15,617 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-08-26 04:47:15,617 INFO Pairs2Cool Resolution [bp]: 50000 2021-08-26 04:47:15,618 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/SRR7500315/__temp__/aligned/inter.pairs.txt" "/tmp/tmp1m_p6fst/inter_no_balanced.cool" 2021-08-26 04:48:25,856 INFO SimpleSubprocess MakeCool - 0:01:10 2021-08-26 04:48:25,857 DEBUG SimpleSubprocess cp "/tmp/tmp1m_p6fst/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-08-26 04:48:25,876 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 04:48:25,879 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_5kb.cool 2021-08-26 04:48:25,880 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_5kb.cool 2021-08-26 04:48:25,880 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-08-26 04:48:25,880 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp3890fx4m/inter.cool" 2021-08-26 04:48:25,912 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 04:48:25,912 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp3890fx4m/inter.cool" "chr1:70,945,000-81,015,000" 2021-08-26 04:48:33,945 INFO SimpleSubprocess NormalizeCool - 0:00:08 2021-08-26 04:48:33,945 DEBUG SimpleSubprocess cp "/tmp/tmp3890fx4m/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_5kb.cool" 2021-08-26 04:48:33,978 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 04:48:33,981 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_10kb.cool 2021-08-26 04:48:33,981 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_10kb.cool 2021-08-26 04:48:33,982 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-08-26 04:48:33,982 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpr4hxcd_g/inter.cool" 2021-08-26 04:48:34,009 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 04:48:34,009 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpr4hxcd_g/inter.cool" "chr1:70,945,000-81,015,000" 2021-08-26 04:48:38,398 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-08-26 04:48:38,399 DEBUG SimpleSubprocess cp "/tmp/tmpr4hxcd_g/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_10kb.cool" 2021-08-26 04:48:38,424 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 04:48:38,427 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_20kb.cool 2021-08-26 04:48:38,427 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_20kb.cool 2021-08-26 04:48:38,427 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-08-26 04:48:38,428 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpw4h_u5rk/inter.cool" 2021-08-26 04:48:38,449 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 04:48:38,449 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpw4h_u5rk/inter.cool" "chr1:70,945,000-81,015,000" 2021-08-26 04:48:41,774 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-08-26 04:48:41,775 DEBUG SimpleSubprocess cp "/tmp/tmpw4h_u5rk/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_20kb.cool" 2021-08-26 04:48:41,798 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 04:48:41,801 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_25kb.cool 2021-08-26 04:48:41,801 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_25kb.cool 2021-08-26 04:48:41,801 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-08-26 04:48:41,801 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmp6rfnre8x/inter.cool" 2021-08-26 04:48:41,823 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 04:48:41,823 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp6rfnre8x/inter.cool" "chr1:70,945,000-81,015,000" 2021-08-26 04:48:44,772 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-08-26 04:48:44,772 DEBUG SimpleSubprocess cp "/tmp/tmp6rfnre8x/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_25kb.cool" 2021-08-26 04:48:44,793 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 04:48:44,795 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_50kb.cool 2021-08-26 04:48:44,795 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_50kb.cool 2021-08-26 04:48:44,795 INFO CTaleNormalize Capture: chr1:70,945,000-81,015,000 2021-08-26 04:48:44,795 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpqvf07w_v/inter.cool" 2021-08-26 04:48:44,813 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 04:48:44,813 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpqvf07w_v/inter.cool" "chr1:70,945,000-81,015,000" 2021-08-26 04:48:46,629 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-08-26 04:48:46,629 DEBUG SimpleSubprocess cp "/tmp/tmpqvf07w_v/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_50kb.cool" 2021-08-26 04:48:46,647 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 04:48:46,651 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/vector.txt 2021-08-26 04:48:46,658 INFO SimpleSubprocess MakeVector - 0:00:00 2021-08-26 04:48:46,658 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_5kb.cool 2021-08-26 04:48:46,658 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/vector.txt 2021-08-26 04:48:46,658 INFO AddWeight Chromosome: chr1 2021-08-26 04:48:46,658 INFO AddWeight Resolution [bp]: 5000 2021-08-26 04:48:46,812 INFO AddWeight AddWeight successfully finished 2021-08-26 04:48:46,812 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_10kb.cool 2021-08-26 04:48:46,813 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/vector.txt 2021-08-26 04:48:46,813 INFO AddWeight Chromosome: chr1 2021-08-26 04:48:46,813 INFO AddWeight Resolution [bp]: 10000 2021-08-26 04:48:46,881 INFO AddWeight AddWeight successfully finished 2021-08-26 04:48:46,881 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_20kb.cool 2021-08-26 04:48:46,881 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/vector.txt 2021-08-26 04:48:46,881 INFO AddWeight Chromosome: chr1 2021-08-26 04:48:46,881 INFO AddWeight Resolution [bp]: 20000 2021-08-26 04:48:46,922 INFO AddWeight AddWeight successfully finished 2021-08-26 04:48:46,923 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_25kb.cool 2021-08-26 04:48:46,923 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/vector.txt 2021-08-26 04:48:46,923 INFO AddWeight Chromosome: chr1 2021-08-26 04:48:46,923 INFO AddWeight Resolution [bp]: 25000 2021-08-26 04:48:46,958 INFO AddWeight AddWeight successfully finished 2021-08-26 04:48:46,958 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_50kb.cool 2021-08-26 04:48:46,958 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/vector.txt 2021-08-26 04:48:46,958 INFO AddWeight Chromosome: chr1 2021-08-26 04:48:46,959 INFO AddWeight Resolution [bp]: 50000 2021-08-26 04:48:46,983 INFO AddWeight AddWeight successfully finished 2021-08-26 04:48:46,985 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter.hic 2021-08-26 04:48:46,985 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_norm.hic 2021-08-26 04:48:46,985 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/vector.txt 2021-08-26 04:48:46,985 INFO Vector2HiC Threads: 10 2021-08-26 04:48:47,016 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter.hic" "/tmp/tmpu41e2_88/inter.hic" 2021-08-26 04:48:47,303 INFO SimpleSubprocess TempFiles - 0:00:00 2021-08-26 04:48:47,303 INFO Vector2HiC Vector: vector c-tale_normalization chr1 5000 BP 2021-08-26 04:48:47,305 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpu41e2_88/inter.hic" "/tmp/tmpu41e2_88/vector.txt" 2021-08-26 04:48:52,656 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-08-26 04:48:52,657 INFO Vector2HiC Vector: vector c-tale_normalization chr1 10000 BP 2021-08-26 04:48:52,658 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpu41e2_88/inter.hic" "/tmp/tmpu41e2_88/vector.txt" 2021-08-26 04:48:56,950 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-08-26 04:48:56,950 INFO Vector2HiC Vector: vector c-tale_normalization chr1 20000 BP 2021-08-26 04:48:56,951 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpu41e2_88/inter.hic" "/tmp/tmpu41e2_88/vector.txt" 2021-08-26 04:49:00,543 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-26 04:49:00,543 INFO Vector2HiC Vector: vector c-tale_normalization chr1 25000 BP 2021-08-26 04:49:00,544 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpu41e2_88/inter.hic" "/tmp/tmpu41e2_88/vector.txt" 2021-08-26 04:49:04,459 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-26 04:49:04,459 INFO Vector2HiC Vector: vector c-tale_normalization chr1 50000 BP 2021-08-26 04:49:04,471 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpu41e2_88/inter.hic" "/tmp/tmpu41e2_88/vector.txt" 2021-08-26 04:49:08,256 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-08-26 04:49:08,257 DEBUG SimpleSubprocess cp "/tmp/tmpu41e2_88/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_norm.hic" 2021-08-26 04:49:08,617 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-08-26 04:49:08,681 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/merged_nodups.txt" 2021-08-26 04:50:48,959 INFO SimpleSubprocess CopyResult - 0:01:40 2021-08-26 04:50:48,959 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter.pairs.txt" 2021-08-26 04:51:00,908 INFO SimpleSubprocess CopyResult - 0:00:11 2021-08-26 04:51:00,929 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/vector.txt" 2021-08-26 04:51:01,088 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:01,089 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter.hic" 2021-08-26 04:51:04,606 INFO SimpleSubprocess CopyResult - 0:00:03 2021-08-26 04:51:04,606 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter_statistics.txt" 2021-08-26 04:51:04,636 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:04,636 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter_no_balanced_5kb.cool" 2021-08-26 04:51:04,805 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:04,805 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter_5kb.cool" 2021-08-26 04:51:05,108 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:05,108 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter_no_balanced_10kb.cool" 2021-08-26 04:51:05,300 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:05,300 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter_10kb.cool" 2021-08-26 04:51:05,475 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:05,475 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter_no_balanced_20kb.cool" 2021-08-26 04:51:05,832 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:05,832 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter_20kb.cool" 2021-08-26 04:51:06,073 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:06,073 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter_no_balanced_25kb.cool" 2021-08-26 04:51:06,218 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:06,219 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter_25kb.cool" 2021-08-26 04:51:06,385 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:06,385 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter_no_balanced_50kb.cool" 2021-08-26 04:51:06,582 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:06,582 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/inter_50kb.cool" 2021-08-26 04:51:06,792 INFO SimpleSubprocess CopyResult - 0:00:00 2021-08-26 04:51:07,037 DEBUG SimpleSubprocess rm -r "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR7500315/__temp__" 2021-08-26 04:51:18,644 INFO SimpleSubprocess RemoveTemp - 0:00:11 2021-08-26 04:51:18,644 INFO BenchmarkPipeline 'SRR7500315' FINISHED, SUMMARY TIME - 9:17:50