2021-09-17 11:24:31,890 INFO BenchmarkPipeline --- START PROCESSING 'SRR6158158-SRR6158159' --- 2021-09-17 11:24:31,890 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158158.sra 2021-09-17 11:24:31,890 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__ 2021-09-17 11:24:31,890 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpg7lzrrie "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158158.sra" 2021-09-17 11:24:34,915 ERROR SimpleSubprocess Command 'Sra2FastQ' has returned non-zero exit code [3] 2021-09-17 11:24:34,915 ERROR SimpleSubprocess Command: fastq-dump --split-3 -O /tmp/tmpg7lzrrie "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158158.sra" 2021-09-17 11:24:34,915 ERROR SimpleSubprocess Details: 2021-09-17T04:24:34 fastq-dump.2.11.0 err: file invalid while opening directory within file system module - failed /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158158.sra ============================================================= An error occurred during processing. A report was generated into the file '/home/fairwind/ncbi_error_report.txt'. If the problem persists, you may consider sending the file to 'sra-tools@ncbi.nlm.nih.gov' for assistance. ============================================================= fastq-dump quit with error code 3 2021-09-20 11:27:07,221 INFO BenchmarkPipeline --- START PROCESSING 'SRR6158158-SRR6158159' --- 2021-09-20 11:27:07,240 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158158.sra 2021-09-20 11:27:07,240 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__ 2021-09-20 11:27:07,240 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpq4mtjwon "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158158.sra" 2021-09-20 11:27:08,230 ERROR SimpleSubprocess Command 'Sra2FastQ' has returned non-zero exit code [3] 2021-09-20 11:27:08,230 ERROR SimpleSubprocess Command: fastq-dump --split-3 -O /tmp/tmpq4mtjwon "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158158.sra" 2021-09-20 11:27:08,230 ERROR SimpleSubprocess Details: 2021-09-20T04:27:08 fastq-dump.2.11.0 err: file invalid while opening directory within file system module - failed /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158158.sra ============================================================= An error occurred during processing. A report was generated into the file '/home/fairwind/ncbi_error_report.txt'. If the problem persists, you may consider sending the file to 'sra-tools@ncbi.nlm.nih.gov' for assistance. ============================================================= fastq-dump quit with error code 3 2021-10-01 09:18:41,229 INFO BenchmarkPipeline --- START PROCESSING 'SRR6158158-SRR6158159' --- 2021-10-01 09:18:41,286 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158158.sra 2021-10-01 09:18:41,286 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__ 2021-10-01 09:18:41,287 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp1yxycg64 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158158.sra" 2021-10-01 09:29:51,909 INFO SimpleSubprocess Sra2FastQ - 0:11:10 2021-10-01 09:29:51,936 DEBUG SimpleSubprocess gzip /tmp/tmp1yxycg64/* 2021-10-01 10:31:47,441 INFO SimpleSubprocess GZipFastQ - 1:01:55 2021-10-01 10:31:47,655 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/fastq"; mv /tmp/tmp1yxycg64/SRR6158158_2.fastq.gz /tmp/tmp1yxycg64/SRR6158158_R2.fastq.gz; mv /tmp/tmp1yxycg64/SRR6158158_1.fastq.gz /tmp/tmp1yxycg64/SRR6158158_R1.fastq.gz; cp /tmp/tmp1yxycg64/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/fastq" 2021-10-01 10:32:32,127 INFO SimpleSubprocess CopyFiles - 0:00:44 2021-10-01 10:32:33,891 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158159.sra 2021-10-01 10:32:33,891 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__ 2021-10-01 10:32:33,891 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpbwms88q9 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6158159.sra" 2021-10-01 10:43:50,394 INFO SimpleSubprocess Sra2FastQ - 0:11:16 2021-10-01 10:43:50,418 DEBUG SimpleSubprocess gzip /tmp/tmpbwms88q9/* 2021-10-01 11:47:26,998 INFO SimpleSubprocess GZipFastQ - 1:03:36 2021-10-01 11:47:26,998 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/fastq"; mv /tmp/tmpbwms88q9/SRR6158159_1.fastq.gz /tmp/tmpbwms88q9/SRR6158159_R1.fastq.gz; mv /tmp/tmpbwms88q9/SRR6158159_2.fastq.gz /tmp/tmpbwms88q9/SRR6158159_R2.fastq.gz; cp /tmp/tmpbwms88q9/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/fastq" 2021-10-01 11:48:17,359 INFO SimpleSubprocess CopyFiles - 0:00:50 2021-10-01 11:48:19,072 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__ 2021-10-01 11:48:19,072 INFO Juicer Genome assembly: mm10 2021-10-01 11:48:19,072 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-10-01 11:48:19,072 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 11:48:19,072 INFO Juicer Enzyme: HindIII 2021-10-01 11:48:19,072 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt 2021-10-01 11:48:19,072 INFO Juicer Threads: 10 2021-10-01 11:48:19,072 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/HIC_tmp" 2021-10-01 11:48:19,102 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-10-01 11:48:19,102 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 HindIII -y "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt" -d "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__" 2021-10-01 21:56:47,707 INFO SimpleSubprocess Juicer - 10:08:28 2021-10-01 21:56:48,173 INFO Juicer Using /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt as site file (-: Looking for fastq files...fastq files exist (-: Aligning files matching /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/fastq/*_R*.fastq* to genome mm10 with site file /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt (-: Created /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/splits/SRR6158158_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/splits/SRR6158158_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/splits/SRR6158158.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/splits/SRR6158158.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/splits/SRR6158159_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/splits/SRR6158159_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/splits/SRR6158159.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/splits/SRR6158159.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 [2021-10-01T18:59:07,626] [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 [2021-10-01T20:40:08,914] [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/SRR6158158-SRR6158159/__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 [2021-10-01T21:56:44,632] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__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/SRR6158158-SRR6158159/__temp__/aligned for results 2021-10-01 21:56:48,552 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/merged_nodups.txt 2021-10-01 21:56:48,552 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt 2021-10-01 21:56:48,748 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpvk3ixlxl/inter.pairs.txt" 2021-10-01 21:58:47,292 INFO SimpleSubprocess MakeInterPairs - 0:01:58 2021-10-01 21:58:47,292 DEBUG SimpleSubprocess cp "/tmp/tmpvk3ixlxl/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt" 2021-10-01 21:58:50,069 INFO SimpleSubprocess CopyFiles - 0:00:02 2021-10-01 21:58:50,585 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt 2021-10-01 21:58:50,585 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_5kb.cool 2021-10-01 21:58:50,585 INFO Pairs2Cool Genome assembly: mm10 2021-10-01 21:58:50,586 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 21:58:50,586 INFO Pairs2Cool Resolution [bp]: 5000 2021-10-01 21:58:50,629 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/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt" "/tmp/tmp04haximj/inter_no_balanced.cool" 2021-10-01 22:02:42,933 INFO SimpleSubprocess MakeCool - 0:03:52 2021-10-01 22:02:42,933 DEBUG SimpleSubprocess cp "/tmp/tmp04haximj/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-10-01 22:02:43,047 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 22:02:43,063 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt 2021-10-01 22:02:43,063 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_10kb.cool 2021-10-01 22:02:43,064 INFO Pairs2Cool Genome assembly: mm10 2021-10-01 22:02:43,064 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 22:02:43,064 INFO Pairs2Cool Resolution [bp]: 10000 2021-10-01 22:02:43,105 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/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt" "/tmp/tmp6w2v3iaa/inter_no_balanced.cool" 2021-10-01 22:06:13,564 INFO SimpleSubprocess MakeCool - 0:03:30 2021-10-01 22:06:13,564 DEBUG SimpleSubprocess cp "/tmp/tmp6w2v3iaa/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-10-01 22:06:13,662 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 22:06:13,701 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt 2021-10-01 22:06:13,701 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_20kb.cool 2021-10-01 22:06:13,701 INFO Pairs2Cool Genome assembly: mm10 2021-10-01 22:06:13,701 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 22:06:13,701 INFO Pairs2Cool Resolution [bp]: 20000 2021-10-01 22:06:13,709 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/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt" "/tmp/tmp8t4nq87h/inter_no_balanced.cool" 2021-10-01 22:09:32,456 INFO SimpleSubprocess MakeCool - 0:03:18 2021-10-01 22:09:32,457 DEBUG SimpleSubprocess cp "/tmp/tmp8t4nq87h/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-10-01 22:09:32,547 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 22:09:32,579 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt 2021-10-01 22:09:32,579 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_25kb.cool 2021-10-01 22:09:32,579 INFO Pairs2Cool Genome assembly: mm10 2021-10-01 22:09:32,579 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 22:09:32,579 INFO Pairs2Cool Resolution [bp]: 25000 2021-10-01 22:09:32,580 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/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt" "/tmp/tmp3tdlyvad/inter_no_balanced.cool" 2021-10-01 22:12:43,769 INFO SimpleSubprocess MakeCool - 0:03:11 2021-10-01 22:12:43,769 DEBUG SimpleSubprocess cp "/tmp/tmp3tdlyvad/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-10-01 22:12:43,846 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 22:12:43,876 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt 2021-10-01 22:12:43,876 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_50kb.cool 2021-10-01 22:12:43,877 INFO Pairs2Cool Genome assembly: mm10 2021-10-01 22:12:43,877 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-10-01 22:12:43,877 INFO Pairs2Cool Resolution [bp]: 50000 2021-10-01 22:12:43,898 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/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt" "/tmp/tmpdjuynbue/inter_no_balanced.cool" 2021-10-01 22:15:42,336 INFO SimpleSubprocess MakeCool - 0:02:58 2021-10-01 22:15:42,337 DEBUG SimpleSubprocess cp "/tmp/tmpdjuynbue/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-10-01 22:15:42,405 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 22:15:42,507 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_5kb.cool 2021-10-01 22:15:42,508 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_5kb.cool 2021-10-01 22:15:42,508 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-10-01 22:15:42,532 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpzjix3nww/inter.cool" 2021-10-01 22:15:42,654 INFO SimpleSubprocess TempFiles - 0:00:00 2021-10-01 22:15:42,654 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpzjix3nww/inter.cool" "chrX:50,550,000-50,675,000" 2021-10-01 22:15:48,795 INFO SimpleSubprocess NormalizeCool - 0:00:06 2021-10-01 22:15:48,795 DEBUG SimpleSubprocess cp "/tmp/tmpzjix3nww/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_5kb.cool" 2021-10-01 22:15:48,908 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 22:15:48,924 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_10kb.cool 2021-10-01 22:15:48,924 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_10kb.cool 2021-10-01 22:15:48,924 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-10-01 22:15:48,943 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp9lx8o18e/inter.cool" 2021-10-01 22:15:49,041 INFO SimpleSubprocess TempFiles - 0:00:00 2021-10-01 22:15:49,041 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp9lx8o18e/inter.cool" "chrX:50,550,000-50,675,000" 2021-10-01 22:15:51,604 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-10-01 22:15:51,604 DEBUG SimpleSubprocess cp "/tmp/tmp9lx8o18e/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_10kb.cool" 2021-10-01 22:15:51,701 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 22:15:51,740 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_20kb.cool 2021-10-01 22:15:51,740 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_20kb.cool 2021-10-01 22:15:51,740 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-10-01 22:15:51,741 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpetgts4cb/inter.cool" 2021-10-01 22:15:51,825 INFO SimpleSubprocess TempFiles - 0:00:00 2021-10-01 22:15:51,825 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpetgts4cb/inter.cool" "chrX:50,550,000-50,675,000" 2021-10-01 22:15:53,816 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-10-01 22:15:53,816 DEBUG SimpleSubprocess cp "/tmp/tmpetgts4cb/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_20kb.cool" 2021-10-01 22:15:53,919 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 22:15:53,955 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_25kb.cool 2021-10-01 22:15:53,955 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_25kb.cool 2021-10-01 22:15:53,955 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-10-01 22:15:53,972 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpvfn1wcx6/inter.cool" 2021-10-01 22:15:54,049 INFO SimpleSubprocess TempFiles - 0:00:00 2021-10-01 22:15:54,049 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpvfn1wcx6/inter.cool" "chrX:50,550,000-50,675,000" 2021-10-01 22:15:55,828 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-10-01 22:15:55,828 DEBUG SimpleSubprocess cp "/tmp/tmpvfn1wcx6/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_25kb.cool" 2021-10-01 22:15:55,905 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 22:15:55,956 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_50kb.cool 2021-10-01 22:15:55,956 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_50kb.cool 2021-10-01 22:15:55,956 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-10-01 22:15:55,956 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmpfhricfw3/inter.cool" 2021-10-01 22:15:56,020 INFO SimpleSubprocess TempFiles - 0:00:00 2021-10-01 22:15:56,020 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpfhricfw3/inter.cool" "chrX:50,550,000-50,675,000" 2021-10-01 22:15:57,504 INFO SimpleSubprocess NormalizeCool - 0:00:01 2021-10-01 22:15:57,505 DEBUG SimpleSubprocess cp "/tmp/tmpfhricfw3/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_50kb.cool" 2021-10-01 22:15:57,567 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-10-01 22:15:57,769 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/vector.txt 2021-10-01 22:15:57,775 INFO SimpleSubprocess MakeVector - 0:00:00 2021-10-01 22:15:57,782 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_5kb.cool 2021-10-01 22:15:57,782 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/vector.txt 2021-10-01 22:15:57,782 INFO AddWeight Chromosome: chrX 2021-10-01 22:15:57,782 INFO AddWeight Resolution [bp]: 5000 2021-10-01 22:16:01,347 INFO AddWeight AddWeight successfully finished 2021-10-01 22:16:01,348 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_10kb.cool 2021-10-01 22:16:01,348 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/vector.txt 2021-10-01 22:16:01,348 INFO AddWeight Chromosome: chrX 2021-10-01 22:16:01,348 INFO AddWeight Resolution [bp]: 10000 2021-10-01 22:16:01,452 INFO AddWeight AddWeight successfully finished 2021-10-01 22:16:01,453 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_20kb.cool 2021-10-01 22:16:01,453 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/vector.txt 2021-10-01 22:16:01,453 INFO AddWeight Chromosome: chrX 2021-10-01 22:16:01,453 INFO AddWeight Resolution [bp]: 20000 2021-10-01 22:16:01,506 INFO AddWeight AddWeight successfully finished 2021-10-01 22:16:01,506 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_25kb.cool 2021-10-01 22:16:01,506 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/vector.txt 2021-10-01 22:16:01,506 INFO AddWeight Chromosome: chrX 2021-10-01 22:16:01,507 INFO AddWeight Resolution [bp]: 25000 2021-10-01 22:16:01,543 INFO AddWeight AddWeight successfully finished 2021-10-01 22:16:01,543 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_50kb.cool 2021-10-01 22:16:01,543 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/vector.txt 2021-10-01 22:16:01,543 INFO AddWeight Chromosome: chrX 2021-10-01 22:16:01,544 INFO AddWeight Resolution [bp]: 50000 2021-10-01 22:16:01,569 INFO AddWeight AddWeight successfully finished 2021-10-01 22:16:01,643 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter.hic 2021-10-01 22:16:01,643 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_norm.hic 2021-10-01 22:16:01,643 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/vector.txt 2021-10-01 22:16:01,643 INFO Vector2HiC Threads: 10 2021-10-01 22:16:01,849 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter.hic" "/tmp/tmpfaabg94u/inter.hic" 2021-10-01 22:16:03,675 INFO SimpleSubprocess TempFiles - 0:00:01 2021-10-01 22:16:03,676 INFO Vector2HiC Vector: vector c-tale_normalization chrX 5000 BP 2021-10-01 22:16:03,677 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpfaabg94u/inter.hic" "/tmp/tmpfaabg94u/vector.txt" 2021-10-01 22:16:08,057 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-10-01 22:16:08,057 INFO Vector2HiC Vector: vector c-tale_normalization chrX 10000 BP 2021-10-01 22:16:08,344 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpfaabg94u/inter.hic" "/tmp/tmpfaabg94u/vector.txt" 2021-10-01 22:16:12,703 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-10-01 22:16:12,703 INFO Vector2HiC Vector: vector c-tale_normalization chrX 20000 BP 2021-10-01 22:16:12,724 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpfaabg94u/inter.hic" "/tmp/tmpfaabg94u/vector.txt" 2021-10-01 22:16:16,611 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-10-01 22:16:16,611 INFO Vector2HiC Vector: vector c-tale_normalization chrX 25000 BP 2021-10-01 22:16:16,612 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpfaabg94u/inter.hic" "/tmp/tmpfaabg94u/vector.txt" 2021-10-01 22:16:20,871 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-10-01 22:16:20,871 INFO Vector2HiC Vector: vector c-tale_normalization chrX 50000 BP 2021-10-01 22:16:20,872 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmpfaabg94u/inter.hic" "/tmp/tmpfaabg94u/vector.txt" 2021-10-01 22:16:24,671 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-10-01 22:16:24,672 DEBUG SimpleSubprocess cp "/tmp/tmpfaabg94u/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_norm.hic" 2021-10-01 22:16:25,691 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-10-01 22:16:25,845 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/merged_nodups.txt" 2021-10-01 22:23:29,225 INFO SimpleSubprocess CopyResult - 0:07:03 2021-10-01 22:23:29,265 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter.pairs.txt" 2021-10-01 22:23:51,079 INFO SimpleSubprocess CopyResult - 0:00:21 2021-10-01 22:23:51,080 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/vector.txt" 2021-10-01 22:23:51,197 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 22:23:51,198 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter.hic" 2021-10-01 22:24:03,708 INFO SimpleSubprocess CopyResult - 0:00:12 2021-10-01 22:24:03,708 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter_statistics.txt" 2021-10-01 22:24:03,761 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 22:24:03,761 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter_no_balanced_5kb.cool" 2021-10-01 22:24:04,849 INFO SimpleSubprocess CopyResult - 0:00:01 2021-10-01 22:24:04,849 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter_5kb.cool" 2021-10-01 22:24:05,986 INFO SimpleSubprocess CopyResult - 0:00:01 2021-10-01 22:24:05,986 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter_no_balanced_10kb.cool" 2021-10-01 22:24:07,203 INFO SimpleSubprocess CopyResult - 0:00:01 2021-10-01 22:24:07,203 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter_10kb.cool" 2021-10-01 22:24:08,908 INFO SimpleSubprocess CopyResult - 0:00:01 2021-10-01 22:24:08,908 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter_no_balanced_20kb.cool" 2021-10-01 22:24:10,144 INFO SimpleSubprocess CopyResult - 0:00:01 2021-10-01 22:24:10,144 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter_20kb.cool" 2021-10-01 22:24:11,133 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 22:24:11,133 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter_no_balanced_25kb.cool" 2021-10-01 22:24:11,849 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 22:24:11,849 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter_25kb.cool" 2021-10-01 22:24:13,018 INFO SimpleSubprocess CopyResult - 0:00:01 2021-10-01 22:24:13,018 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter_no_balanced_50kb.cool" 2021-10-01 22:24:13,852 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 22:24:13,853 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/inter_50kb.cool" 2021-10-01 22:24:14,656 INFO SimpleSubprocess CopyResult - 0:00:00 2021-10-01 22:24:14,739 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6158158-SRR6158159/__temp__" 2021-10-01 22:24:32,743 INFO SimpleSubprocess RemoveTemp - 0:00:18 2021-10-01 22:24:32,743 INFO BenchmarkPipeline 'SRR6158158-SRR6158159' FINISHED, SUMMARY TIME - 13:05:51