2021-09-30 23:32:31,139 INFO BenchmarkPipeline --- START PROCESSING 'SRR8984915-SRR8984916' --- 2021-09-30 23:32:31,139 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984915.sra 2021-09-30 23:32:31,139 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__ 2021-09-30 23:32:31,139 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpiyx4t8an "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984915.sra" 2021-09-30 23:44:46,299 INFO SimpleSubprocess Sra2FastQ - 0:12:15 2021-09-30 23:44:46,299 DEBUG SimpleSubprocess gzip /tmp/tmpiyx4t8an/* 2021-10-01 00:28:01,234 INFO SimpleSubprocess GZipFastQ - 0:43:14 2021-10-01 00:28:01,283 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/fastq"; mv /tmp/tmpiyx4t8an/SRR8984915_2.fastq.gz /tmp/tmpiyx4t8an/SRR8984915_R2.fastq.gz; mv /tmp/tmpiyx4t8an/SRR8984915_1.fastq.gz /tmp/tmpiyx4t8an/SRR8984915_R1.fastq.gz; cp /tmp/tmpiyx4t8an/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/fastq" 2021-10-01 00:28:09,163 INFO SimpleSubprocess CopyFiles - 0:00:07 2021-10-01 00:28:10,295 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984916.sra 2021-10-01 00:28:10,295 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__ 2021-10-01 00:28:10,295 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpb580a9yy "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR8984916.sra" 2021-10-01 00:42:32,938 INFO SimpleSubprocess Sra2FastQ - 0:14:22 2021-10-01 00:42:32,955 DEBUG SimpleSubprocess gzip /tmp/tmpb580a9yy/* 2021-10-01 01:33:28,496 INFO SimpleSubprocess GZipFastQ - 0:50:55 2021-10-01 01:33:28,497 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/fastq"; mv /tmp/tmpb580a9yy/SRR8984916_2.fastq.gz /tmp/tmpb580a9yy/SRR8984916_R2.fastq.gz; mv /tmp/tmpb580a9yy/SRR8984916_1.fastq.gz /tmp/tmpb580a9yy/SRR8984916_R1.fastq.gz; cp /tmp/tmpb580a9yy/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/fastq" 2021-10-01 01:33:40,879 INFO SimpleSubprocess CopyFiles - 0:00:12 2021-10-01 01:33:42,341 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__ 2021-10-01 01:33:42,341 INFO Juicer Genome assembly: mm10 2021-10-01 01:33:42,341 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-10-01 01:33:42,341 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 01:33:42,341 INFO Juicer Enzyme: DpnII 2021-10-01 01:33:42,341 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-10-01 01:33:42,341 INFO Juicer Threads: 10 2021-10-01 01:33:42,341 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/HIC_tmp" 2021-10-01 01:33:42,377 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-10-01 01:33:42,377 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/SRR8984915-SRR8984916/__temp__" 2021-10-01 09:09:02,270 INFO SimpleSubprocess Juicer - 7:35:19 2021-10-01 09:09:02,561 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/SRR8984915-SRR8984916/__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/SRR8984915-SRR8984916/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/splits/SRR8984915_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/splits/SRR8984915_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/splits/SRR8984915.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/splits/SRR8984915.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/splits/SRR8984916_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/splits/SRR8984916_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/splits/SRR8984916.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/splits/SRR8984916.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 [2021-10-01T07:54:03,520] [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 [2021-10-01T08:33:39,298] [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/SRR8984915-SRR8984916/__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 [2021-10-01T09:09:00,935] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__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/SRR8984915-SRR8984916/__temp__/aligned for results 2021-10-01 09:09:02,858 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/merged_nodups.txt 2021-10-01 09:09:02,858 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt 2021-10-01 09:09:03,082 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp2bcssk5y/inter.pairs.txt" 2021-10-01 09:09:57,449 INFO SimpleSubprocess MakeInterPairs - 0:00:54 2021-10-01 09:09:57,449 DEBUG SimpleSubprocess cp "/tmp/tmp2bcssk5y/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt" 2021-10-01 09:09:58,809 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-10-01 09:09:59,630 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt 2021-10-01 09:09:59,630 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_5kb.cool 2021-10-01 09:09:59,630 INFO Pairs2Cool Genome assembly: mm10 2021-10-01 09:09:59,630 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 09:09:59,630 INFO Pairs2Cool Resolution [bp]: 5000 2021-10-01 09:09:59,631 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/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt" "/tmp/tmpqrqa0l4d/inter_no_balanced.cool" 2021-10-01 09:11:28,165 INFO SimpleSubprocess MakeCool - 0:01:28 2021-10-01 09:11:28,165 DEBUG SimpleSubprocess cp "/tmp/tmpqrqa0l4d/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-10-01 09:11:28,198 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 09:11:28,256 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt 2021-10-01 09:11:28,256 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_10kb.cool 2021-10-01 09:11:28,256 INFO Pairs2Cool Genome assembly: mm10 2021-10-01 09:11:28,256 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 09:11:28,256 INFO Pairs2Cool Resolution [bp]: 10000 2021-10-01 09:11:28,257 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/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt" "/tmp/tmpdwknjpuj/inter_no_balanced.cool" 2021-10-01 09:12:45,607 INFO SimpleSubprocess MakeCool - 0:01:17 2021-10-01 09:12:45,607 DEBUG SimpleSubprocess cp "/tmp/tmpdwknjpuj/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-10-01 09:12:45,634 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 09:12:45,663 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt 2021-10-01 09:12:45,663 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_20kb.cool 2021-10-01 09:12:45,663 INFO Pairs2Cool Genome assembly: mm10 2021-10-01 09:12:45,663 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 09:12:45,663 INFO Pairs2Cool Resolution [bp]: 20000 2021-10-01 09:12:45,671 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/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt" "/tmp/tmpkp0vk5zl/inter_no_balanced.cool" 2021-10-01 09:13:58,168 INFO SimpleSubprocess MakeCool - 0:01:12 2021-10-01 09:13:58,168 DEBUG SimpleSubprocess cp "/tmp/tmpkp0vk5zl/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-10-01 09:13:58,192 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 09:13:58,239 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt 2021-10-01 09:13:58,239 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_25kb.cool 2021-10-01 09:13:58,239 INFO Pairs2Cool Genome assembly: mm10 2021-10-01 09:13:58,239 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 09:13:58,239 INFO Pairs2Cool Resolution [bp]: 25000 2021-10-01 09:13:58,265 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/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt" "/tmp/tmpds2jodka/inter_no_balanced.cool" 2021-10-01 09:15:07,858 INFO SimpleSubprocess MakeCool - 0:01:09 2021-10-01 09:15:07,859 DEBUG SimpleSubprocess cp "/tmp/tmpds2jodka/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-10-01 09:15:07,880 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 09:15:07,914 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt 2021-10-01 09:15:07,914 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_50kb.cool 2021-10-01 09:15:07,914 INFO Pairs2Cool Genome assembly: mm10 2021-10-01 09:15:07,914 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 09:15:07,914 INFO Pairs2Cool Resolution [bp]: 50000 2021-10-01 09:15:07,945 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/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt" "/tmp/tmpy_5po3ww/inter_no_balanced.cool" 2021-10-01 09:16:12,334 INFO SimpleSubprocess MakeCool - 0:01:04 2021-10-01 09:16:12,334 DEBUG SimpleSubprocess cp "/tmp/tmpy_5po3ww/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-10-01 09:16:12,353 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 09:16:12,448 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_5kb.cool 2021-10-01 09:16:12,449 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_5kb.cool 2021-10-01 09:16:12,449 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-10-01 09:16:12,449 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmp1vcl83lv/inter.cool" 2021-10-01 09:16:12,486 INFO SimpleSubprocess TempFiles - 0:00:00 2021-10-01 09:16:12,486 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp1vcl83lv/inter.cool" "chr5:27,460,000-30,345,000" 2021-10-01 09:16:30,111 INFO SimpleSubprocess NormalizeCool - 0:00:17 2021-10-01 09:16:30,111 DEBUG SimpleSubprocess cp "/tmp/tmp1vcl83lv/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_5kb.cool" 2021-10-01 09:16:30,143 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 09:16:30,146 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_10kb.cool 2021-10-01 09:16:30,147 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_10kb.cool 2021-10-01 09:16:30,147 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-10-01 09:16:30,147 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp794pnnqt/inter.cool" 2021-10-01 09:16:30,173 INFO SimpleSubprocess TempFiles - 0:00:00 2021-10-01 09:16:30,174 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp794pnnqt/inter.cool" "chr5:27,460,000-30,345,000" 2021-10-01 09:16:41,795 INFO SimpleSubprocess NormalizeCool - 0:00:11 2021-10-01 09:16:41,796 DEBUG SimpleSubprocess cp "/tmp/tmp794pnnqt/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_10kb.cool" 2021-10-01 09:16:41,822 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 09:16:41,826 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_20kb.cool 2021-10-01 09:16:41,826 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_20kb.cool 2021-10-01 09:16:41,826 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-10-01 09:16:41,826 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpg83_uq1w/inter.cool" 2021-10-01 09:16:41,849 INFO SimpleSubprocess TempFiles - 0:00:00 2021-10-01 09:16:41,849 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpg83_uq1w/inter.cool" "chr5:27,460,000-30,345,000" 2021-10-01 09:16:49,059 INFO SimpleSubprocess NormalizeCool - 0:00:07 2021-10-01 09:16:49,059 DEBUG SimpleSubprocess cp "/tmp/tmpg83_uq1w/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_20kb.cool" 2021-10-01 09:16:49,082 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 09:16:49,131 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_25kb.cool 2021-10-01 09:16:49,131 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_25kb.cool 2021-10-01 09:16:49,131 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-10-01 09:16:49,154 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpx1nl8bxn/inter.cool" 2021-10-01 09:16:49,175 INFO SimpleSubprocess TempFiles - 0:00:00 2021-10-01 09:16:49,176 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpx1nl8bxn/inter.cool" "chr5:27,460,000-30,345,000" 2021-10-01 09:16:55,321 INFO SimpleSubprocess NormalizeCool - 0:00:06 2021-10-01 09:16:55,322 DEBUG SimpleSubprocess cp "/tmp/tmpx1nl8bxn/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_25kb.cool" 2021-10-01 09:16:55,341 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 09:16:55,344 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_50kb.cool 2021-10-01 09:16:55,344 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_50kb.cool 2021-10-01 09:16:55,344 INFO CTaleNormalize Capture: chr5:27,460,000-30,345,000 2021-10-01 09:16:55,366 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpi4v25yq4/inter.cool" 2021-10-01 09:16:55,384 INFO SimpleSubprocess TempFiles - 0:00:00 2021-10-01 09:16:55,384 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpi4v25yq4/inter.cool" "chr5:27,460,000-30,345,000" 2021-10-01 09:16:58,926 INFO SimpleSubprocess NormalizeCool - 0:00:03 2021-10-01 09:16:58,926 DEBUG SimpleSubprocess cp "/tmp/tmpi4v25yq4/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_50kb.cool" 2021-10-01 09:16:58,944 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 09:16:59,001 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/vector.txt 2021-10-01 09:16:59,007 INFO SimpleSubprocess MakeVector - 0:00:00 2021-10-01 09:16:59,038 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_5kb.cool 2021-10-01 09:16:59,038 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/vector.txt 2021-10-01 09:16:59,038 INFO AddWeight Chromosome: chr5 2021-10-01 09:16:59,038 INFO AddWeight Resolution [bp]: 5000 2021-10-01 09:17:03,979 INFO AddWeight AddWeight successfully finished 2021-10-01 09:17:03,979 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_10kb.cool 2021-10-01 09:17:03,979 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/vector.txt 2021-10-01 09:17:03,979 INFO AddWeight Chromosome: chr5 2021-10-01 09:17:03,979 INFO AddWeight Resolution [bp]: 10000 2021-10-01 09:17:04,032 INFO AddWeight AddWeight successfully finished 2021-10-01 09:17:04,033 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_20kb.cool 2021-10-01 09:17:04,033 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/vector.txt 2021-10-01 09:17:04,033 INFO AddWeight Chromosome: chr5 2021-10-01 09:17:04,033 INFO AddWeight Resolution [bp]: 20000 2021-10-01 09:17:04,065 INFO AddWeight AddWeight successfully finished 2021-10-01 09:17:04,065 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_25kb.cool 2021-10-01 09:17:04,065 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/vector.txt 2021-10-01 09:17:04,065 INFO AddWeight Chromosome: chr5 2021-10-01 09:17:04,065 INFO AddWeight Resolution [bp]: 25000 2021-10-01 09:17:04,089 INFO AddWeight AddWeight successfully finished 2021-10-01 09:17:04,089 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_50kb.cool 2021-10-01 09:17:04,089 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/vector.txt 2021-10-01 09:17:04,089 INFO AddWeight Chromosome: chr5 2021-10-01 09:17:04,089 INFO AddWeight Resolution [bp]: 50000 2021-10-01 09:17:04,116 INFO AddWeight AddWeight successfully finished 2021-10-01 09:17:04,118 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter.hic 2021-10-01 09:17:04,118 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_norm.hic 2021-10-01 09:17:04,118 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/vector.txt 2021-10-01 09:17:04,118 INFO Vector2HiC Threads: 10 2021-10-01 09:17:04,206 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter.hic" "/tmp/tmpsjp_vir3/inter.hic" 2021-10-01 09:17:04,494 INFO SimpleSubprocess TempFiles - 0:00:00 2021-10-01 09:17:04,495 INFO Vector2HiC Vector: vector c-tale_normalization chr5 5000 BP 2021-10-01 09:17:04,496 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpsjp_vir3/inter.hic" "/tmp/tmpsjp_vir3/vector.txt" 2021-10-01 09:17:09,083 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-10-01 09:17:09,083 INFO Vector2HiC Vector: vector c-tale_normalization chr5 10000 BP 2021-10-01 09:17:09,084 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpsjp_vir3/inter.hic" "/tmp/tmpsjp_vir3/vector.txt" 2021-10-01 09:17:13,384 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-10-01 09:17:13,384 INFO Vector2HiC Vector: vector c-tale_normalization chr5 20000 BP 2021-10-01 09:17:13,384 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpsjp_vir3/inter.hic" "/tmp/tmpsjp_vir3/vector.txt" 2021-10-01 09:17:17,169 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-10-01 09:17:17,169 INFO Vector2HiC Vector: vector c-tale_normalization chr5 25000 BP 2021-10-01 09:17:17,170 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpsjp_vir3/inter.hic" "/tmp/tmpsjp_vir3/vector.txt" 2021-10-01 09:17:21,146 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-10-01 09:17:21,146 INFO Vector2HiC Vector: vector c-tale_normalization chr5 50000 BP 2021-10-01 09:17:21,147 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpsjp_vir3/inter.hic" "/tmp/tmpsjp_vir3/vector.txt" 2021-10-01 09:17:25,221 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-10-01 09:17:25,222 DEBUG SimpleSubprocess cp "/tmp/tmpsjp_vir3/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_norm.hic" 2021-10-01 09:17:25,595 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 09:17:25,655 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/merged_nodups.txt" 2021-10-01 09:18:06,396 INFO SimpleSubprocess CopyResult - 0:00:40 2021-10-01 09:18:06,396 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter.pairs.txt" 2021-10-01 09:18:18,191 INFO SimpleSubprocess CopyResult - 0:00:11 2021-10-01 09:18:18,191 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/vector.txt" 2021-10-01 09:18:18,199 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:18,199 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter.hic" 2021-10-01 09:18:21,023 INFO SimpleSubprocess CopyResult - 0:00:02 2021-10-01 09:18:21,023 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter_statistics.txt" 2021-10-01 09:18:21,032 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:21,032 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter_no_balanced_5kb.cool" 2021-10-01 09:18:21,228 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:21,228 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter_5kb.cool" 2021-10-01 09:18:21,427 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:21,428 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter_no_balanced_10kb.cool" 2021-10-01 09:18:21,580 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:21,580 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter_10kb.cool" 2021-10-01 09:18:21,732 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:21,732 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter_no_balanced_20kb.cool" 2021-10-01 09:18:21,867 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:21,867 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter_20kb.cool" 2021-10-01 09:18:21,957 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:21,957 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter_no_balanced_25kb.cool" 2021-10-01 09:18:22,047 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:22,047 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter_25kb.cool" 2021-10-01 09:18:22,163 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:22,163 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter_no_balanced_50kb.cool" 2021-10-01 09:18:22,247 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:22,248 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/inter_50kb.cool" 2021-10-01 09:18:22,347 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 09:18:22,452 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR8984915-SRR8984916/__temp__" 2021-10-01 09:18:40,610 INFO SimpleSubprocess RemoveTemp - 0:00:18 2021-10-01 09:18:40,610 INFO BenchmarkPipeline 'SRR8984915-SRR8984916' FINISHED, SUMMARY TIME - 9:46:09