2021-09-07 07:04:11,065 INFO BenchmarkPipeline --- START PROCESSING 'SRR6024987-SRR6024988' --- 2021-09-07 07:04:11,065 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024987.sra 2021-09-07 07:04:11,065 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__ 2021-09-07 07:04:11,066 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmplnw_q3gc "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024987.sra" 2021-09-07 07:18:25,128 INFO SimpleSubprocess Sra2FastQ - 0:14:14 2021-09-07 07:18:25,128 DEBUG SimpleSubprocess gzip /tmp/tmplnw_q3gc/* 2021-09-07 07:50:42,756 INFO SimpleSubprocess GZipFastQ - 0:32:17 2021-09-07 07:50:42,922 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/fastq"; mv /tmp/tmplnw_q3gc/SRR6024987_1.fastq.gz /tmp/tmplnw_q3gc/SRR6024987_R1.fastq.gz; mv /tmp/tmplnw_q3gc/SRR6024987_2.fastq.gz /tmp/tmplnw_q3gc/SRR6024987_R2.fastq.gz; cp /tmp/tmplnw_q3gc/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/fastq" 2021-09-07 07:50:49,153 INFO SimpleSubprocess CopyFiles - 0:00:06 2021-09-07 07:50:50,095 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024988.sra 2021-09-07 07:50:50,095 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__ 2021-09-07 07:50:50,116 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpub6om80p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6024988.sra" 2021-09-07 08:04:53,855 INFO SimpleSubprocess Sra2FastQ - 0:14:03 2021-09-07 08:04:53,870 DEBUG SimpleSubprocess gzip /tmp/tmpub6om80p/* 2021-09-07 08:36:50,268 INFO SimpleSubprocess GZipFastQ - 0:31:56 2021-09-07 08:36:50,268 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/fastq"; mv /tmp/tmpub6om80p/SRR6024988_2.fastq.gz /tmp/tmpub6om80p/SRR6024988_R2.fastq.gz; mv /tmp/tmpub6om80p/SRR6024988_1.fastq.gz /tmp/tmpub6om80p/SRR6024988_R1.fastq.gz; cp /tmp/tmpub6om80p/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/fastq" 2021-09-07 08:36:56,498 INFO SimpleSubprocess CopyFiles - 0:00:06 2021-09-07 08:36:57,427 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__ 2021-09-07 08:36:57,427 INFO Juicer Genome assembly: mm10 2021-09-07 08:36:57,427 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-07 08:36:57,427 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-07 08:36:57,427 INFO Juicer Enzyme: DpnII 2021-09-07 08:36:57,427 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-07 08:36:57,427 INFO Juicer Threads: 10 2021-09-07 08:36:57,427 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/splits" 2021-09-07 08:36:57,471 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-07 08:36:57,471 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/SRR6024987-SRR6024988/__temp__" 2021-09-07 16:33:03,049 INFO SimpleSubprocess Juicer - 7:56:05 2021-09-07 16:33:03,078 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/SRR6024987-SRR6024988/__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/SRR6024987-SRR6024988/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/splits/SRR6024987_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/splits/SRR6024987_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/splits/SRR6024987.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/splits/SRR6024987.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/splits/SRR6024988_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/splits/SRR6024988_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/splits/SRR6024988.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/splits/SRR6024988.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 [2021-09-07T15:25:21,028] [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 [2021-09-07T16:02:52,681] [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/SRR6024987-SRR6024988/__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 [2021-09-07T16:33:02,596] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__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/SRR6024987-SRR6024988/__temp__/aligned for results 2021-09-07 16:33:03,106 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/merged_nodups.txt 2021-09-07 16:33:03,106 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt 2021-09-07 16:33:03,160 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpjkgbw3o6/inter.pairs.txt" 2021-09-07 16:34:13,472 INFO SimpleSubprocess MakeInterPairs - 0:01:10 2021-09-07 16:34:13,472 DEBUG SimpleSubprocess cp "/tmp/tmpjkgbw3o6/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt" 2021-09-07 16:34:15,299 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-07 16:34:15,568 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt 2021-09-07 16:34:15,569 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-07 16:34:15,569 INFO Pairs2Cool Genome assembly: mm10 2021-09-07 16:34:15,569 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-07 16:34:15,569 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-07 16:34:15,569 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/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt" "/tmp/tmpevxe2xec/inter_no_balanced.cool" 2021-09-07 16:36:14,399 INFO SimpleSubprocess MakeCool - 0:01:58 2021-09-07 16:36:14,399 DEBUG SimpleSubprocess cp "/tmp/tmpevxe2xec/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-07 16:36:14,447 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 16:36:14,453 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt 2021-09-07 16:36:14,453 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-07 16:36:14,453 INFO Pairs2Cool Genome assembly: mm10 2021-09-07 16:36:14,453 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-07 16:36:14,453 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-07 16:36:14,454 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/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt" "/tmp/tmp0aa7s6ay/inter_no_balanced.cool" 2021-09-07 16:38:00,726 INFO SimpleSubprocess MakeCool - 0:01:46 2021-09-07 16:38:00,727 DEBUG SimpleSubprocess cp "/tmp/tmp0aa7s6ay/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-07 16:38:00,766 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 16:38:01,155 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt 2021-09-07 16:38:01,156 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-07 16:38:01,156 INFO Pairs2Cool Genome assembly: mm10 2021-09-07 16:38:01,156 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-07 16:38:01,156 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-07 16:38:01,156 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/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt" "/tmp/tmpk3gvtna9/inter_no_balanced.cool" 2021-09-07 16:39:43,854 INFO SimpleSubprocess MakeCool - 0:01:42 2021-09-07 16:39:43,854 DEBUG SimpleSubprocess cp "/tmp/tmpk3gvtna9/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-07 16:39:43,891 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 16:39:43,897 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt 2021-09-07 16:39:43,897 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-07 16:39:43,897 INFO Pairs2Cool Genome assembly: mm10 2021-09-07 16:39:43,897 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-07 16:39:43,897 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-07 16:39:43,897 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/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt" "/tmp/tmpp2tfuz8o/inter_no_balanced.cool" 2021-09-07 16:41:23,073 INFO SimpleSubprocess MakeCool - 0:01:39 2021-09-07 16:41:23,073 DEBUG SimpleSubprocess cp "/tmp/tmpp2tfuz8o/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-07 16:41:23,108 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 16:41:23,113 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt 2021-09-07 16:41:23,114 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-07 16:41:23,114 INFO Pairs2Cool Genome assembly: mm10 2021-09-07 16:41:23,114 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-07 16:41:23,114 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-07 16:41:23,145 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/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt" "/tmp/tmpdall2z1e/inter_no_balanced.cool" 2021-09-07 16:42:57,531 INFO SimpleSubprocess MakeCool - 0:01:34 2021-09-07 16:42:57,531 DEBUG SimpleSubprocess cp "/tmp/tmpdall2z1e/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-07 16:42:57,559 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 16:42:57,564 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-07 16:42:57,564 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_5kb.cool 2021-09-07 16:42:57,564 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-07 16:42:57,565 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpdaqtd7ys/inter.cool" 2021-09-07 16:42:57,610 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 16:42:57,610 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpdaqtd7ys/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-07 16:43:02,087 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-09-07 16:43:02,087 DEBUG SimpleSubprocess cp "/tmp/tmpdaqtd7ys/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_5kb.cool" 2021-09-07 16:43:02,132 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 16:43:02,165 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-07 16:43:02,165 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_10kb.cool 2021-09-07 16:43:02,165 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-07 16:43:02,193 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpb9ohnxi8/inter.cool" 2021-09-07 16:43:02,233 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 16:43:02,233 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpb9ohnxi8/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-07 16:43:04,630 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-07 16:43:04,630 DEBUG SimpleSubprocess cp "/tmp/tmpb9ohnxi8/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_10kb.cool" 2021-09-07 16:43:04,669 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 16:43:04,953 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-07 16:43:04,953 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_20kb.cool 2021-09-07 16:43:04,953 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-07 16:43:04,983 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpbflv57sc/inter.cool" 2021-09-07 16:43:05,020 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 16:43:05,021 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpbflv57sc/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-07 16:43:06,853 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-07 16:43:06,854 DEBUG SimpleSubprocess cp "/tmp/tmpbflv57sc/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_20kb.cool" 2021-09-07 16:43:06,891 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 16:43:06,896 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-07 16:43:06,897 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_25kb.cool 2021-09-07 16:43:06,897 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-07 16:43:06,899 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpl_s8e9m7/inter.cool" 2021-09-07 16:43:06,934 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 16:43:06,935 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpl_s8e9m7/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-07 16:43:08,604 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-07 16:43:08,604 DEBUG SimpleSubprocess cp "/tmp/tmpl_s8e9m7/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_25kb.cool" 2021-09-07 16:43:08,639 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 16:43:08,644 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-07 16:43:08,644 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_50kb.cool 2021-09-07 16:43:08,644 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-07 16:43:08,674 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmp4wwceycp/inter.cool" 2021-09-07 16:43:08,704 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 16:43:08,704 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp4wwceycp/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-07 16:43:11,579 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-07 16:43:11,579 DEBUG SimpleSubprocess cp "/tmp/tmp4wwceycp/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_50kb.cool" 2021-09-07 16:43:11,608 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 16:43:11,639 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/vector.txt 2021-09-07 16:43:11,645 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-07 16:43:11,645 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_5kb.cool 2021-09-07 16:43:11,645 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/vector.txt 2021-09-07 16:43:11,645 INFO AddWeight Chromosome: chr13 2021-09-07 16:43:11,645 INFO AddWeight Resolution [bp]: 5000 2021-09-07 16:43:11,799 INFO AddWeight AddWeight successfully finished 2021-09-07 16:43:11,799 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_10kb.cool 2021-09-07 16:43:11,799 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/vector.txt 2021-09-07 16:43:11,799 INFO AddWeight Chromosome: chr13 2021-09-07 16:43:11,799 INFO AddWeight Resolution [bp]: 10000 2021-09-07 16:43:11,852 INFO AddWeight AddWeight successfully finished 2021-09-07 16:43:11,852 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_20kb.cool 2021-09-07 16:43:11,852 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/vector.txt 2021-09-07 16:43:11,852 INFO AddWeight Chromosome: chr13 2021-09-07 16:43:11,852 INFO AddWeight Resolution [bp]: 20000 2021-09-07 16:43:11,886 INFO AddWeight AddWeight successfully finished 2021-09-07 16:43:11,886 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_25kb.cool 2021-09-07 16:43:11,886 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/vector.txt 2021-09-07 16:43:11,886 INFO AddWeight Chromosome: chr13 2021-09-07 16:43:11,886 INFO AddWeight Resolution [bp]: 25000 2021-09-07 16:43:11,916 INFO AddWeight AddWeight successfully finished 2021-09-07 16:43:11,917 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_50kb.cool 2021-09-07 16:43:11,917 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/vector.txt 2021-09-07 16:43:11,917 INFO AddWeight Chromosome: chr13 2021-09-07 16:43:11,917 INFO AddWeight Resolution [bp]: 50000 2021-09-07 16:43:11,939 INFO AddWeight AddWeight successfully finished 2021-09-07 16:43:11,941 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter.hic 2021-09-07 16:43:11,941 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_norm.hic 2021-09-07 16:43:11,941 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/vector.txt 2021-09-07 16:43:11,941 INFO Vector2HiC Threads: 10 2021-09-07 16:43:11,963 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter.hic" "/tmp/tmp5795imrm/inter.hic" 2021-09-07 16:43:12,318 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-07 16:43:12,318 INFO Vector2HiC Vector: vector c-tale_normalization chr13 5000 BP 2021-09-07 16:43:12,319 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp5795imrm/inter.hic" "/tmp/tmp5795imrm/vector.txt" 2021-09-07 16:43:17,064 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-07 16:43:17,065 INFO Vector2HiC Vector: vector c-tale_normalization chr13 10000 BP 2021-09-07 16:43:17,066 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp5795imrm/inter.hic" "/tmp/tmp5795imrm/vector.txt" 2021-09-07 16:43:21,180 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-07 16:43:21,181 INFO Vector2HiC Vector: vector c-tale_normalization chr13 20000 BP 2021-09-07 16:43:21,181 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp5795imrm/inter.hic" "/tmp/tmp5795imrm/vector.txt" 2021-09-07 16:43:24,885 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-07 16:43:24,885 INFO Vector2HiC Vector: vector c-tale_normalization chr13 25000 BP 2021-09-07 16:43:24,886 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp5795imrm/inter.hic" "/tmp/tmp5795imrm/vector.txt" 2021-09-07 16:43:28,802 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-07 16:43:28,803 INFO Vector2HiC Vector: vector c-tale_normalization chr13 50000 BP 2021-09-07 16:43:28,803 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp5795imrm/inter.hic" "/tmp/tmp5795imrm/vector.txt" 2021-09-07 16:43:32,604 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-07 16:43:32,604 DEBUG SimpleSubprocess cp "/tmp/tmp5795imrm/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_norm.hic" 2021-09-07 16:43:33,017 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-07 16:43:33,088 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/merged_nodups.txt" 2021-09-07 16:44:29,135 INFO SimpleSubprocess CopyResult - 0:00:56 2021-09-07 16:44:29,136 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter.pairs.txt" 2021-09-07 16:44:44,191 INFO SimpleSubprocess CopyResult - 0:00:15 2021-09-07 16:44:44,192 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/vector.txt" 2021-09-07 16:44:44,201 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:44,201 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter.hic" 2021-09-07 16:44:48,051 INFO SimpleSubprocess CopyResult - 0:00:03 2021-09-07 16:44:48,051 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter_statistics.txt" 2021-09-07 16:44:48,058 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:48,058 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter_no_balanced_5kb.cool" 2021-09-07 16:44:48,316 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:48,316 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter_5kb.cool" 2021-09-07 16:44:48,672 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:48,672 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter_no_balanced_10kb.cool" 2021-09-07 16:44:48,978 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:48,979 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter_10kb.cool" 2021-09-07 16:44:49,286 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:49,287 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter_no_balanced_20kb.cool" 2021-09-07 16:44:49,547 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:49,548 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter_20kb.cool" 2021-09-07 16:44:49,804 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:49,804 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter_no_balanced_25kb.cool" 2021-09-07 16:44:50,047 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:50,047 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter_25kb.cool" 2021-09-07 16:44:50,291 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:50,291 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter_no_balanced_50kb.cool" 2021-09-07 16:44:50,487 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:50,487 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/inter_50kb.cool" 2021-09-07 16:44:50,635 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-07 16:44:50,671 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__" 2021-09-07 16:45:04,573 INFO SimpleSubprocess RemoveTemp - 0:00:13 2021-09-07 16:45:04,573 INFO BenchmarkPipeline 'SRR6024987-SRR6024988' FINISHED, SUMMARY TIME - 9:40:53 2021-09-10 13:00:59,254 INFO BenchmarkPipeline --- START PROCESSING 'SRR6024987-SRR6024988' --- 2021-09-10 13:00:59,272 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6024987-SRR6024988/__temp__" 2021-09-10 13:00:59,282 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-10 13:00:59,282 INFO BenchmarkPipeline 'SRR6024987-SRR6024988' FINISHED, SUMMARY TIME - 0:00:00