2021-09-22 00:49:13,000 INFO BenchmarkPipeline --- START PROCESSING 'SRR6451287-SRR7203995' --- 2021-09-22 00:49:13,007 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6451287.sra 2021-09-22 00:49:13,007 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__ 2021-09-22 00:49:13,016 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp11_21v8l "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6451287.sra" 2021-09-22 01:06:13,188 INFO SimpleSubprocess Sra2FastQ - 0:17:00 2021-09-22 01:06:13,222 DEBUG SimpleSubprocess gzip /tmp/tmp11_21v8l/* 2021-09-22 02:08:03,756 INFO SimpleSubprocess GZipFastQ - 1:01:50 2021-09-22 02:08:03,988 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/fastq"; mv /tmp/tmp11_21v8l/SRR6451287_2.fastq.gz /tmp/tmp11_21v8l/SRR6451287_R2.fastq.gz; mv /tmp/tmp11_21v8l/SRR6451287_1.fastq.gz /tmp/tmp11_21v8l/SRR6451287_R1.fastq.gz; cp /tmp/tmp11_21v8l/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/fastq" 2021-09-22 02:08:30,501 INFO SimpleSubprocess CopyFiles - 0:00:26 2021-09-22 02:08:31,909 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7203995.sra 2021-09-22 02:08:31,909 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__ 2021-09-22 02:08:31,940 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpbrl4m3gw "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR7203995.sra" 2021-09-22 02:42:11,287 INFO SimpleSubprocess Sra2FastQ - 0:33:39 2021-09-22 02:42:11,308 DEBUG SimpleSubprocess gzip /tmp/tmpbrl4m3gw/* 2021-09-22 03:59:47,233 INFO SimpleSubprocess GZipFastQ - 1:17:35 2021-09-22 03:59:47,251 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/fastq"; mv /tmp/tmpbrl4m3gw/SRR7203995_2.fastq.gz /tmp/tmpbrl4m3gw/SRR7203995_R2.fastq.gz; mv /tmp/tmpbrl4m3gw/SRR7203995_1.fastq.gz /tmp/tmpbrl4m3gw/SRR7203995_R1.fastq.gz; cp /tmp/tmpbrl4m3gw/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/fastq" 2021-09-22 04:00:49,140 INFO SimpleSubprocess CopyFiles - 0:01:01 2021-09-22 04:00:50,731 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__ 2021-09-22 04:00:50,731 INFO Juicer Genome assembly: mm10 2021-09-22 04:00:50,732 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-22 04:00:50,732 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 04:00:50,732 INFO Juicer Enzyme: DpnII 2021-09-22 04:00:50,732 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_DpnII_mm10.txt 2021-09-22 04:00:50,732 INFO Juicer Threads: 10 2021-09-22 04:00:50,732 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/HIC_tmp" 2021-09-22 04:00:50,769 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-22 04:00:50,769 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/SRR6451287-SRR7203995/__temp__" 2021-09-22 16:47:37,177 INFO SimpleSubprocess Juicer - 12:46:46 2021-09-22 16:47:37,192 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/SRR6451287-SRR7203995/__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/SRR6451287-SRR7203995/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/splits/SRR6451287_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/splits/SRR6451287_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/splits/SRR6451287.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/splits/SRR6451287.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/splits/SRR7203995_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/splits/SRR7203995_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/splits/SRR7203995.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/splits/SRR7203995.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 [2021-09-22T15:32:58,085] [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 [2021-09-22T16:20:33,659] [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/SRR6451287-SRR7203995/__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 [2021-09-22T16:47:36,861] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__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/SRR6451287-SRR7203995/__temp__/aligned for results 2021-09-22 16:47:37,211 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/merged_nodups.txt 2021-09-22 16:47:37,212 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt 2021-09-22 16:47:37,212 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/merged_nodups.txt" > "/tmp/tmp9ujy55x2/inter.pairs.txt" 2021-09-22 16:48:35,133 INFO SimpleSubprocess MakeInterPairs - 0:00:57 2021-09-22 16:48:35,133 DEBUG SimpleSubprocess cp "/tmp/tmp9ujy55x2/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt" 2021-09-22 16:48:36,627 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-22 16:48:36,838 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt 2021-09-22 16:48:36,838 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-22 16:48:36,838 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 16:48:36,838 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 16:48:36,838 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-22 16:48:36,906 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/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt" "/tmp/tmp3vp02b0s/inter_no_balanced.cool" 2021-09-22 16:50:16,484 INFO SimpleSubprocess MakeCool - 0:01:39 2021-09-22 16:50:16,484 DEBUG SimpleSubprocess cp "/tmp/tmp3vp02b0s/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-22 16:50:16,523 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 16:50:16,528 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt 2021-09-22 16:50:16,528 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-22 16:50:16,528 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 16:50:16,528 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 16:50:16,528 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-22 16:50:16,552 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/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt" "/tmp/tmpwljzecf7/inter_no_balanced.cool" 2021-09-22 16:51:44,838 INFO SimpleSubprocess MakeCool - 0:01:28 2021-09-22 16:51:44,838 DEBUG SimpleSubprocess cp "/tmp/tmpwljzecf7/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-22 16:51:44,871 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 16:51:44,875 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt 2021-09-22 16:51:44,876 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-22 16:51:44,876 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 16:51:44,876 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 16:51:44,876 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-22 16:51:44,876 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/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt" "/tmp/tmpkp3rq758/inter_no_balanced.cool" 2021-09-22 16:53:07,935 INFO SimpleSubprocess MakeCool - 0:01:23 2021-09-22 16:53:07,936 DEBUG SimpleSubprocess cp "/tmp/tmpkp3rq758/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-22 16:53:07,965 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 16:53:07,969 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt 2021-09-22 16:53:07,969 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-22 16:53:07,969 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 16:53:07,969 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 16:53:07,969 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-22 16:53:07,969 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/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt" "/tmp/tmpt16etgcj/inter_no_balanced.cool" 2021-09-22 16:54:29,883 INFO SimpleSubprocess MakeCool - 0:01:21 2021-09-22 16:54:29,884 DEBUG SimpleSubprocess cp "/tmp/tmpt16etgcj/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-22 16:54:29,913 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 16:54:29,916 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt 2021-09-22 16:54:29,916 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-22 16:54:29,917 INFO Pairs2Cool Genome assembly: mm10 2021-09-22 16:54:29,917 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-22 16:54:29,917 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-22 16:54:29,917 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/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt" "/tmp/tmp_lg_a0a4/inter_no_balanced.cool" 2021-09-22 16:55:43,856 INFO SimpleSubprocess MakeCool - 0:01:13 2021-09-22 16:55:43,857 DEBUG SimpleSubprocess cp "/tmp/tmp_lg_a0a4/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-22 16:55:43,878 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 16:55:43,883 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-22 16:55:43,883 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_5kb.cool 2021-09-22 16:55:43,883 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-22 16:55:43,942 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmprfmhalc9/inter.cool" 2021-09-22 16:55:43,981 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 16:55:43,981 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmprfmhalc9/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-22 16:55:49,095 INFO SimpleSubprocess NormalizeCool - 0:00:05 2021-09-22 16:55:49,095 DEBUG SimpleSubprocess cp "/tmp/tmprfmhalc9/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_5kb.cool" 2021-09-22 16:55:49,164 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 16:55:49,169 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-22 16:55:49,169 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_10kb.cool 2021-09-22 16:55:49,169 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-22 16:55:49,170 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp3746qviq/inter.cool" 2021-09-22 16:55:49,203 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 16:55:49,203 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp3746qviq/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-22 16:55:51,893 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-22 16:55:51,893 DEBUG SimpleSubprocess cp "/tmp/tmp3746qviq/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_10kb.cool" 2021-09-22 16:55:51,926 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 16:55:51,930 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-22 16:55:51,930 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_20kb.cool 2021-09-22 16:55:51,930 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-22 16:55:51,931 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpsnc5_gcl/inter.cool" 2021-09-22 16:55:51,960 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 16:55:51,960 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpsnc5_gcl/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-22 16:55:53,731 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-22 16:55:53,731 DEBUG SimpleSubprocess cp "/tmp/tmpsnc5_gcl/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_20kb.cool" 2021-09-22 16:55:53,761 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 16:55:53,764 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-22 16:55:53,764 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_25kb.cool 2021-09-22 16:55:53,765 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-22 16:55:53,787 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmp34cfg8xs/inter.cool" 2021-09-22 16:55:53,814 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 16:55:53,814 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp34cfg8xs/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-22 16:55:55,376 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-22 16:55:55,377 DEBUG SimpleSubprocess cp "/tmp/tmp34cfg8xs/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_25kb.cool" 2021-09-22 16:55:55,404 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 16:55:55,407 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-22 16:55:55,407 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_50kb.cool 2021-09-22 16:55:55,407 INFO CTaleNormalize Capture: chr13:53,895,001-57,200,000 2021-09-22 16:55:55,407 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpn_ksh_eb/inter.cool" 2021-09-22 16:55:55,429 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 16:55:55,429 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpn_ksh_eb/inter.cool" "chr13:53,895,001-57,200,000" 2021-09-22 16:55:56,559 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-09-22 16:55:56,560 DEBUG SimpleSubprocess cp "/tmp/tmpn_ksh_eb/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_50kb.cool" 2021-09-22 16:55:56,583 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 16:55:56,588 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/vector.txt 2021-09-22 16:55:56,595 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-22 16:55:56,595 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_5kb.cool 2021-09-22 16:55:56,595 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/vector.txt 2021-09-22 16:55:56,595 INFO AddWeight Chromosome: chr13 2021-09-22 16:55:56,595 INFO AddWeight Resolution [bp]: 5000 2021-09-22 16:55:56,701 INFO AddWeight AddWeight successfully finished 2021-09-22 16:55:56,702 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_10kb.cool 2021-09-22 16:55:56,702 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/vector.txt 2021-09-22 16:55:56,702 INFO AddWeight Chromosome: chr13 2021-09-22 16:55:56,702 INFO AddWeight Resolution [bp]: 10000 2021-09-22 16:55:56,794 INFO AddWeight AddWeight successfully finished 2021-09-22 16:55:56,795 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_20kb.cool 2021-09-22 16:55:56,795 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/vector.txt 2021-09-22 16:55:56,795 INFO AddWeight Chromosome: chr13 2021-09-22 16:55:56,795 INFO AddWeight Resolution [bp]: 20000 2021-09-22 16:55:56,826 INFO AddWeight AddWeight successfully finished 2021-09-22 16:55:56,826 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_25kb.cool 2021-09-22 16:55:56,826 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/vector.txt 2021-09-22 16:55:56,826 INFO AddWeight Chromosome: chr13 2021-09-22 16:55:56,826 INFO AddWeight Resolution [bp]: 25000 2021-09-22 16:55:56,853 INFO AddWeight AddWeight successfully finished 2021-09-22 16:55:56,853 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_50kb.cool 2021-09-22 16:55:56,853 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/vector.txt 2021-09-22 16:55:56,853 INFO AddWeight Chromosome: chr13 2021-09-22 16:55:56,854 INFO AddWeight Resolution [bp]: 50000 2021-09-22 16:55:56,874 INFO AddWeight AddWeight successfully finished 2021-09-22 16:55:56,876 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter.hic 2021-09-22 16:55:56,876 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_norm.hic 2021-09-22 16:55:56,876 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/vector.txt 2021-09-22 16:55:56,876 INFO Vector2HiC Threads: 10 2021-09-22 16:55:56,895 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter.hic" "/tmp/tmpkbt71za4/inter.hic" 2021-09-22 16:55:57,238 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-22 16:55:57,238 INFO Vector2HiC Vector: vector c-tale_normalization chr13 5000 BP 2021-09-22 16:55:57,239 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkbt71za4/inter.hic" "/tmp/tmpkbt71za4/vector.txt" 2021-09-22 16:56:01,935 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-22 16:56:01,935 INFO Vector2HiC Vector: vector c-tale_normalization chr13 10000 BP 2021-09-22 16:56:01,936 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkbt71za4/inter.hic" "/tmp/tmpkbt71za4/vector.txt" 2021-09-22 16:56:06,106 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-22 16:56:06,107 INFO Vector2HiC Vector: vector c-tale_normalization chr13 20000 BP 2021-09-22 16:56:06,107 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkbt71za4/inter.hic" "/tmp/tmpkbt71za4/vector.txt" 2021-09-22 16:56:09,758 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-22 16:56:09,758 INFO Vector2HiC Vector: vector c-tale_normalization chr13 25000 BP 2021-09-22 16:56:09,758 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkbt71za4/inter.hic" "/tmp/tmpkbt71za4/vector.txt" 2021-09-22 16:56:13,451 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-22 16:56:13,451 INFO Vector2HiC Vector: vector c-tale_normalization chr13 50000 BP 2021-09-22 16:56:13,451 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpkbt71za4/inter.hic" "/tmp/tmpkbt71za4/vector.txt" 2021-09-22 16:56:17,158 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-22 16:56:17,159 DEBUG SimpleSubprocess cp "/tmp/tmpkbt71za4/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_norm.hic" 2021-09-22 16:56:17,534 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-22 16:56:17,594 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/merged_nodups.txt" 2021-09-22 16:56:59,808 INFO SimpleSubprocess CopyResult - 0:00:42 2021-09-22 16:56:59,808 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter.pairs.txt" 2021-09-22 16:57:12,753 INFO SimpleSubprocess CopyResult - 0:00:12 2021-09-22 16:57:12,753 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/vector.txt" 2021-09-22 16:57:12,762 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:12,762 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter.hic" 2021-09-22 16:57:15,927 INFO SimpleSubprocess CopyResult - 0:00:03 2021-09-22 16:57:15,927 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter_statistics.txt" 2021-09-22 16:57:15,935 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:15,935 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter_no_balanced_5kb.cool" 2021-09-22 16:57:16,211 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:16,211 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter_5kb.cool" 2021-09-22 16:57:16,466 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:16,467 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter_no_balanced_10kb.cool" 2021-09-22 16:57:16,676 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:16,676 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter_10kb.cool" 2021-09-22 16:57:16,875 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:16,875 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter_no_balanced_20kb.cool" 2021-09-22 16:57:17,071 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:17,071 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter_20kb.cool" 2021-09-22 16:57:17,267 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:17,267 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter_no_balanced_25kb.cool" 2021-09-22 16:57:17,432 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:17,432 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter_25kb.cool" 2021-09-22 16:57:17,596 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:17,596 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter_no_balanced_50kb.cool" 2021-09-22 16:57:17,712 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:17,712 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/inter_50kb.cool" 2021-09-22 16:57:17,831 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-22 16:57:18,107 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6451287-SRR7203995/__temp__" 2021-09-22 16:57:36,993 INFO SimpleSubprocess RemoveTemp - 0:00:18 2021-09-22 16:57:36,993 INFO BenchmarkPipeline 'SRR6451287-SRR7203995' FINISHED, SUMMARY TIME - 16:08:23