2021-09-24 11:05:59,653 INFO BenchmarkPipeline --- START PROCESSING 'SRR8284497-SRR8284498' --- 2021-09-24 11:05:59,653 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284497.sra 2021-09-24 11:05:59,653 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__ 2021-09-24 11:05:59,653 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmptl3k6lz7 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284497.sra" 2021-09-24 11:26:05,170 INFO SimpleSubprocess Sra2FastQ - 0:20:05 2021-09-24 11:26:05,183 DEBUG SimpleSubprocess gzip /tmp/tmptl3k6lz7/* 2021-09-24 12:28:54,932 INFO SimpleSubprocess GZipFastQ - 1:02:49 2021-09-24 12:28:54,933 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/fastq"; mv /tmp/tmptl3k6lz7/SRR8284497_2.fastq.gz /tmp/tmptl3k6lz7/SRR8284497_R2.fastq.gz; mv /tmp/tmptl3k6lz7/SRR8284497_1.fastq.gz /tmp/tmptl3k6lz7/SRR8284497_R1.fastq.gz; cp /tmp/tmptl3k6lz7/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/fastq" 2021-09-24 12:29:24,692 INFO SimpleSubprocess CopyFiles - 0:00:29 2021-09-24 12:29:26,211 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284498.sra 2021-09-24 12:29:26,211 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__ 2021-09-24 12:29:26,211 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpmmh0fyqs "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8284498.sra" 2021-09-24 12:49:18,220 INFO SimpleSubprocess Sra2FastQ - 0:19:52 2021-09-24 12:49:18,237 DEBUG SimpleSubprocess gzip /tmp/tmpmmh0fyqs/* 2021-09-24 13:49:36,660 INFO SimpleSubprocess GZipFastQ - 1:00:18 2021-09-24 13:49:36,661 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/fastq"; mv /tmp/tmpmmh0fyqs/SRR8284498_2.fastq.gz /tmp/tmpmmh0fyqs/SRR8284498_R2.fastq.gz; mv /tmp/tmpmmh0fyqs/SRR8284498_1.fastq.gz /tmp/tmpmmh0fyqs/SRR8284498_R1.fastq.gz; cp /tmp/tmpmmh0fyqs/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/fastq" 2021-09-24 13:50:03,693 INFO SimpleSubprocess CopyFiles - 0:00:27 2021-09-24 13:50:05,179 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__ 2021-09-24 13:50:05,179 INFO Juicer Genome assembly: mm10 2021-09-24 13:50:05,179 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-24 13:50:05,179 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-24 13:50:05,179 INFO Juicer Enzyme: DpnII 2021-09-24 13:50:05,179 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-24 13:50:05,179 INFO Juicer Threads: 10 2021-09-24 13:50:05,179 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/HIC_tmp" 2021-09-24 13:50:05,188 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-24 13:50:05,188 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/SRR8284497-SRR8284498/__temp__" 2021-09-25 02:44:52,963 INFO SimpleSubprocess Juicer - 12:54:47 2021-09-25 02:44:53,023 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/SRR8284497-SRR8284498/__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/SRR8284497-SRR8284498/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/splits/SRR8284497_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/splits/SRR8284497_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/splits/SRR8284497.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/splits/SRR8284497.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/splits/SRR8284498_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/splits/SRR8284498_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/splits/SRR8284498.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/splits/SRR8284498.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 [2021-09-25T00:59:18,050] [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 [2021-09-25T02:00:15,436] [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/SRR8284497-SRR8284498/__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 [2021-09-25T02:44:52,148] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__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/SRR8284497-SRR8284498/__temp__/aligned for results 2021-09-25 02:44:53,145 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/merged_nodups.txt 2021-09-25 02:44:53,145 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt 2021-09-25 02:44:53,159 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpavc80l2n/inter.pairs.txt" 2021-09-25 02:47:07,598 INFO SimpleSubprocess MakeInterPairs - 0:02:14 2021-09-25 02:47:07,598 DEBUG SimpleSubprocess cp "/tmp/tmpavc80l2n/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt" 2021-09-25 02:47:11,037 INFO SimpleSubprocess CopyFiles - 0:00:03 2021-09-25 02:47:12,143 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt 2021-09-25 02:47:12,143 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-25 02:47:12,143 INFO Pairs2Cool Genome assembly: mm10 2021-09-25 02:47:12,143 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-25 02:47:12,143 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-25 02:47:12,218 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/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt" "/tmp/tmpr7zi7j_c/inter_no_balanced.cool" 2021-09-25 02:50:34,323 INFO SimpleSubprocess MakeCool - 0:03:22 2021-09-25 02:50:34,324 DEBUG SimpleSubprocess cp "/tmp/tmpr7zi7j_c/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-25 02:50:34,424 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 02:50:34,434 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt 2021-09-25 02:50:34,434 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-25 02:50:34,434 INFO Pairs2Cool Genome assembly: mm10 2021-09-25 02:50:34,434 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-25 02:50:34,434 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-25 02:50:34,484 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/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt" "/tmp/tmphz_uncy3/inter_no_balanced.cool" 2021-09-25 02:53:34,227 INFO SimpleSubprocess MakeCool - 0:02:59 2021-09-25 02:53:34,227 DEBUG SimpleSubprocess cp "/tmp/tmphz_uncy3/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-25 02:53:34,288 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 02:53:34,296 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt 2021-09-25 02:53:34,296 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-25 02:53:34,296 INFO Pairs2Cool Genome assembly: mm10 2021-09-25 02:53:34,296 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-25 02:53:34,296 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-25 02:53:34,296 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/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt" "/tmp/tmpwten7p5c/inter_no_balanced.cool" 2021-09-25 02:56:24,325 INFO SimpleSubprocess MakeCool - 0:02:50 2021-09-25 02:56:24,325 DEBUG SimpleSubprocess cp "/tmp/tmpwten7p5c/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-25 02:56:24,375 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 02:56:24,381 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt 2021-09-25 02:56:24,382 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-25 02:56:24,382 INFO Pairs2Cool Genome assembly: mm10 2021-09-25 02:56:24,382 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-25 02:56:24,382 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-25 02:56:24,382 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/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt" "/tmp/tmpz7ln0lvi/inter_no_balanced.cool" 2021-09-25 02:59:11,287 INFO SimpleSubprocess MakeCool - 0:02:46 2021-09-25 02:59:11,287 DEBUG SimpleSubprocess cp "/tmp/tmpz7ln0lvi/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-25 02:59:11,333 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 02:59:11,371 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt 2021-09-25 02:59:11,371 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-25 02:59:11,371 INFO Pairs2Cool Genome assembly: mm10 2021-09-25 02:59:11,371 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-25 02:59:11,371 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-25 02:59:11,371 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/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt" "/tmp/tmp7ccfhfi8/inter_no_balanced.cool" 2021-09-25 03:01:54,037 INFO SimpleSubprocess MakeCool - 0:02:42 2021-09-25 03:01:54,037 DEBUG SimpleSubprocess cp "/tmp/tmp7ccfhfi8/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-25 03:01:54,076 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 03:01:54,083 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-25 03:01:54,083 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_5kb.cool 2021-09-25 03:01:54,083 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-25 03:01:54,111 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpptzro9pi/inter.cool" 2021-09-25 03:01:54,176 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 03:01:54,176 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpptzro9pi/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-25 03:02:10,244 INFO SimpleSubprocess NormalizeCool - 0:00:16 2021-09-25 03:02:10,244 DEBUG SimpleSubprocess cp "/tmp/tmpptzro9pi/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_5kb.cool" 2021-09-25 03:02:10,345 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 03:02:10,354 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-25 03:02:10,354 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_10kb.cool 2021-09-25 03:02:10,354 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-25 03:02:10,381 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmpbdiv_6ey/inter.cool" 2021-09-25 03:02:10,516 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 03:02:10,517 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpbdiv_6ey/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-25 03:02:22,136 INFO SimpleSubprocess NormalizeCool - 0:00:11 2021-09-25 03:02:22,137 DEBUG SimpleSubprocess cp "/tmp/tmpbdiv_6ey/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_10kb.cool" 2021-09-25 03:02:22,196 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 03:02:22,234 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-25 03:02:22,234 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_20kb.cool 2021-09-25 03:02:22,234 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-25 03:02:22,266 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpwymxfbkd/inter.cool" 2021-09-25 03:02:22,318 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 03:02:22,318 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpwymxfbkd/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-25 03:02:30,219 INFO SimpleSubprocess NormalizeCool - 0:00:07 2021-09-25 03:02:30,219 DEBUG SimpleSubprocess cp "/tmp/tmpwymxfbkd/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_20kb.cool" 2021-09-25 03:02:30,273 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 03:02:30,280 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-25 03:02:30,280 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_25kb.cool 2021-09-25 03:02:30,280 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-25 03:02:30,281 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpkbiiuh7k/inter.cool" 2021-09-25 03:02:30,328 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 03:02:30,328 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpkbiiuh7k/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-25 03:02:37,857 INFO SimpleSubprocess NormalizeCool - 0:00:07 2021-09-25 03:02:37,857 DEBUG SimpleSubprocess cp "/tmp/tmpkbiiuh7k/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_25kb.cool" 2021-09-25 03:02:37,903 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 03:02:37,908 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-25 03:02:37,908 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_50kb.cool 2021-09-25 03:02:37,908 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-09-25 03:02:37,974 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpvvc0i7yh/inter.cool" 2021-09-25 03:02:38,013 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 03:02:38,013 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpvvc0i7yh/inter.cool" "chr5:27,460,000-30,345,000" 2021-09-25 03:02:42,284 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-09-25 03:02:42,285 DEBUG SimpleSubprocess cp "/tmp/tmpvvc0i7yh/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_50kb.cool" 2021-09-25 03:02:42,325 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 03:02:42,393 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/vector.txt 2021-09-25 03:02:42,400 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-25 03:02:42,400 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_5kb.cool 2021-09-25 03:02:42,400 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/vector.txt 2021-09-25 03:02:42,401 INFO AddWeight Chromosome: chr5 2021-09-25 03:02:42,401 INFO AddWeight Resolution [bp]: 5000 2021-09-25 03:02:43,727 INFO AddWeight AddWeight successfully finished 2021-09-25 03:02:43,727 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_10kb.cool 2021-09-25 03:02:43,727 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/vector.txt 2021-09-25 03:02:43,727 INFO AddWeight Chromosome: chr5 2021-09-25 03:02:43,727 INFO AddWeight Resolution [bp]: 10000 2021-09-25 03:02:43,767 INFO AddWeight AddWeight successfully finished 2021-09-25 03:02:43,767 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_20kb.cool 2021-09-25 03:02:43,767 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/vector.txt 2021-09-25 03:02:43,768 INFO AddWeight Chromosome: chr5 2021-09-25 03:02:43,768 INFO AddWeight Resolution [bp]: 20000 2021-09-25 03:02:43,795 INFO AddWeight AddWeight successfully finished 2021-09-25 03:02:43,795 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_25kb.cool 2021-09-25 03:02:43,795 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/vector.txt 2021-09-25 03:02:43,795 INFO AddWeight Chromosome: chr5 2021-09-25 03:02:43,795 INFO AddWeight Resolution [bp]: 25000 2021-09-25 03:02:43,825 INFO AddWeight AddWeight successfully finished 2021-09-25 03:02:43,826 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_50kb.cool 2021-09-25 03:02:43,826 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/vector.txt 2021-09-25 03:02:43,826 INFO AddWeight Chromosome: chr5 2021-09-25 03:02:43,826 INFO AddWeight Resolution [bp]: 50000 2021-09-25 03:02:43,845 INFO AddWeight AddWeight successfully finished 2021-09-25 03:02:43,847 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter.hic 2021-09-25 03:02:43,847 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_norm.hic 2021-09-25 03:02:43,847 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/vector.txt 2021-09-25 03:02:43,847 INFO Vector2HiC Threads: 10 2021-09-25 03:02:43,923 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter.hic" "/tmp/tmp2qdb5l4v/inter.hic" 2021-09-25 03:02:44,390 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-25 03:02:44,391 INFO Vector2HiC Vector: vector c-tale_normalization chr5 5000 BP 2021-09-25 03:02:44,392 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp2qdb5l4v/inter.hic" "/tmp/tmp2qdb5l4v/vector.txt" 2021-09-25 03:02:49,449 INFO SimpleSubprocess NormalizeHiC - 0:00:05 2021-09-25 03:02:49,449 INFO Vector2HiC Vector: vector c-tale_normalization chr5 10000 BP 2021-09-25 03:02:49,450 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp2qdb5l4v/inter.hic" "/tmp/tmp2qdb5l4v/vector.txt" 2021-09-25 03:02:53,910 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-25 03:02:53,911 INFO Vector2HiC Vector: vector c-tale_normalization chr5 20000 BP 2021-09-25 03:02:53,911 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp2qdb5l4v/inter.hic" "/tmp/tmp2qdb5l4v/vector.txt" 2021-09-25 03:02:57,902 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-25 03:02:57,902 INFO Vector2HiC Vector: vector c-tale_normalization chr5 25000 BP 2021-09-25 03:02:57,903 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp2qdb5l4v/inter.hic" "/tmp/tmp2qdb5l4v/vector.txt" 2021-09-25 03:03:02,236 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-25 03:03:02,236 INFO Vector2HiC Vector: vector c-tale_normalization chr5 50000 BP 2021-09-25 03:03:02,237 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp2qdb5l4v/inter.hic" "/tmp/tmp2qdb5l4v/vector.txt" 2021-09-25 03:03:06,473 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-25 03:03:06,473 DEBUG SimpleSubprocess cp "/tmp/tmp2qdb5l4v/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_norm.hic" 2021-09-25 03:03:07,002 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-25 03:03:07,084 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/merged_nodups.txt" 2021-09-25 03:08:04,697 INFO SimpleSubprocess CopyResult - 0:04:57 2021-09-25 03:08:04,993 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter.pairs.txt" 2021-09-25 03:08:31,778 INFO SimpleSubprocess CopyResult - 0:00:26 2021-09-25 03:08:31,779 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/vector.txt" 2021-09-25 03:08:31,841 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 03:08:31,841 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter.hic" 2021-09-25 03:08:38,040 INFO SimpleSubprocess CopyResult - 0:00:06 2021-09-25 03:08:38,040 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter_statistics.txt" 2021-09-25 03:08:38,133 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 03:08:38,134 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter_no_balanced_5kb.cool" 2021-09-25 03:08:39,196 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-25 03:08:39,196 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter_5kb.cool" 2021-09-25 03:08:40,164 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 03:08:40,165 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter_no_balanced_10kb.cool" 2021-09-25 03:08:40,552 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 03:08:40,552 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter_10kb.cool" 2021-09-25 03:08:41,053 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 03:08:41,054 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter_no_balanced_20kb.cool" 2021-09-25 03:08:41,542 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 03:08:41,543 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter_20kb.cool" 2021-09-25 03:08:41,880 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 03:08:41,880 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter_no_balanced_25kb.cool" 2021-09-25 03:08:42,255 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 03:08:42,255 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter_25kb.cool" 2021-09-25 03:08:42,622 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 03:08:42,623 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter_no_balanced_50kb.cool" 2021-09-25 03:08:42,996 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 03:08:42,996 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/inter_50kb.cool" 2021-09-25 03:08:43,255 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-25 03:08:43,278 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8284497-SRR8284498/__temp__" 2021-09-25 03:09:14,062 INFO SimpleSubprocess RemoveTemp - 0:00:30 2021-09-25 03:09:14,063 INFO BenchmarkPipeline 'SRR8284497-SRR8284498' FINISHED, SUMMARY TIME - 16:03:14