2021-09-12 22:55:48,033 INFO BenchmarkPipeline --- START PROCESSING 'SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104' --- 2021-09-12 22:55:48,033 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129098.sra 2021-09-12 22:55:48,034 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__ 2021-09-12 22:55:48,034 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpoupta28t "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129098.sra" 2021-09-12 23:15:38,581 INFO SimpleSubprocess Sra2FastQ - 0:19:50 2021-09-12 23:15:38,617 DEBUG SimpleSubprocess gzip /tmp/tmpoupta28t/* 2021-09-13 00:43:43,470 INFO SimpleSubprocess GZipFastQ - 1:28:04 2021-09-13 00:43:44,081 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq"; mv /tmp/tmpoupta28t/SRR6129098_1.fastq.gz /tmp/tmpoupta28t/SRR6129098_R1.fastq.gz; mv /tmp/tmpoupta28t/SRR6129098_2.fastq.gz /tmp/tmpoupta28t/SRR6129098_R2.fastq.gz; cp /tmp/tmpoupta28t/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq" 2021-09-13 00:45:22,920 INFO SimpleSubprocess CopyFiles - 0:01:38 2021-09-13 00:45:24,733 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129099.sra 2021-09-13 00:45:24,733 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__ 2021-09-13 00:45:24,733 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpuemsd1ib "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129099.sra" 2021-09-13 01:04:55,719 INFO SimpleSubprocess Sra2FastQ - 0:19:30 2021-09-13 01:04:55,760 DEBUG SimpleSubprocess gzip /tmp/tmpuemsd1ib/* 2021-09-13 02:33:49,374 INFO SimpleSubprocess GZipFastQ - 1:28:53 2021-09-13 02:33:49,390 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq"; mv /tmp/tmpuemsd1ib/SRR6129099_2.fastq.gz /tmp/tmpuemsd1ib/SRR6129099_R2.fastq.gz; mv /tmp/tmpuemsd1ib/SRR6129099_1.fastq.gz /tmp/tmpuemsd1ib/SRR6129099_R1.fastq.gz; cp /tmp/tmpuemsd1ib/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq" 2021-09-13 02:35:24,501 INFO SimpleSubprocess CopyFiles - 0:01:35 2021-09-13 02:35:26,320 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129100.sra 2021-09-13 02:35:26,320 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__ 2021-09-13 02:35:26,354 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpym1lyv41 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129100.sra" 2021-09-13 02:44:16,916 INFO SimpleSubprocess Sra2FastQ - 0:08:50 2021-09-13 02:44:16,948 DEBUG SimpleSubprocess gzip /tmp/tmpym1lyv41/* 2021-09-13 03:29:38,674 INFO SimpleSubprocess GZipFastQ - 0:45:21 2021-09-13 03:29:38,675 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq"; mv /tmp/tmpym1lyv41/SRR6129100_2.fastq.gz /tmp/tmpym1lyv41/SRR6129100_R2.fastq.gz; mv /tmp/tmpym1lyv41/SRR6129100_1.fastq.gz /tmp/tmpym1lyv41/SRR6129100_R1.fastq.gz; cp /tmp/tmpym1lyv41/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq" 2021-09-13 03:29:49,059 INFO SimpleSubprocess CopyFiles - 0:00:10 2021-09-13 03:29:50,276 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129101.sra 2021-09-13 03:29:50,277 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__ 2021-09-13 03:29:50,303 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp0mldj577 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129101.sra" 2021-09-13 03:38:28,345 INFO SimpleSubprocess Sra2FastQ - 0:08:38 2021-09-13 03:38:28,362 DEBUG SimpleSubprocess gzip /tmp/tmp0mldj577/* 2021-09-13 04:16:20,059 INFO SimpleSubprocess GZipFastQ - 0:37:51 2021-09-13 04:16:20,059 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq"; mv /tmp/tmp0mldj577/SRR6129101_2.fastq.gz /tmp/tmp0mldj577/SRR6129101_R2.fastq.gz; mv /tmp/tmp0mldj577/SRR6129101_1.fastq.gz /tmp/tmp0mldj577/SRR6129101_R1.fastq.gz; cp /tmp/tmp0mldj577/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq" 2021-09-13 04:16:30,559 INFO SimpleSubprocess CopyFiles - 0:00:10 2021-09-13 04:16:31,667 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129102.sra 2021-09-13 04:16:31,667 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__ 2021-09-13 04:16:31,689 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpc8k56msa "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129102.sra" 2021-09-13 04:25:25,150 INFO SimpleSubprocess Sra2FastQ - 0:08:53 2021-09-13 04:25:25,174 DEBUG SimpleSubprocess gzip /tmp/tmpc8k56msa/* 2021-09-13 05:03:31,693 INFO SimpleSubprocess GZipFastQ - 0:38:06 2021-09-13 05:03:31,706 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq"; mv /tmp/tmpc8k56msa/SRR6129102_1.fastq.gz /tmp/tmpc8k56msa/SRR6129102_R1.fastq.gz; mv /tmp/tmpc8k56msa/SRR6129102_2.fastq.gz /tmp/tmpc8k56msa/SRR6129102_R2.fastq.gz; cp /tmp/tmpc8k56msa/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq" 2021-09-13 05:03:42,344 INFO SimpleSubprocess CopyFiles - 0:00:10 2021-09-13 05:03:43,576 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129103.sra 2021-09-13 05:03:43,576 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__ 2021-09-13 05:03:43,603 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmpzc24cy5x "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129103.sra" 2021-09-13 05:04:31,530 INFO SimpleSubprocess Sra2FastQ - 0:00:47 2021-09-13 05:04:31,531 DEBUG SimpleSubprocess gzip /tmp/tmpzc24cy5x/* 2021-09-13 05:06:19,131 INFO SimpleSubprocess GZipFastQ - 0:01:47 2021-09-13 05:06:19,132 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq"; mv /tmp/tmpzc24cy5x/SRR6129103_1.fastq.gz /tmp/tmpzc24cy5x/SRR6129103_R1.fastq.gz; mv /tmp/tmpzc24cy5x/SRR6129103_2.fastq.gz /tmp/tmpzc24cy5x/SRR6129103_R2.fastq.gz; cp /tmp/tmpzc24cy5x/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq" 2021-09-13 05:06:19,574 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-13 05:06:19,634 INFO Sra2FastQ Accession: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129104.sra 2021-09-13 05:06:19,635 INFO Sra2FastQ Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__ 2021-09-13 05:06:19,666 DEBUG SimpleSubprocess fastq-dump --split-3 -O /tmp/tmp3rxrpma7 "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Source/SRR6129104.sra" 2021-09-13 05:29:50,527 INFO SimpleSubprocess Sra2FastQ - 0:23:30 2021-09-13 05:29:50,549 DEBUG SimpleSubprocess gzip /tmp/tmp3rxrpma7/* 2021-09-13 07:00:17,528 INFO SimpleSubprocess GZipFastQ - 1:30:26 2021-09-13 07:00:17,542 DEBUG SimpleSubprocess mkdir -p "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq"; mv /tmp/tmp3rxrpma7/SRR6129104_1.fastq.gz /tmp/tmp3rxrpma7/SRR6129104_R1.fastq.gz; mv /tmp/tmp3rxrpma7/SRR6129104_2.fastq.gz /tmp/tmp3rxrpma7/SRR6129104_R2.fastq.gz; cp /tmp/tmp3rxrpma7/*_R*.fastq* "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/fastq" 2021-09-13 07:02:20,703 INFO SimpleSubprocess CopyFiles - 0:02:03 2021-09-13 07:02:22,546 INFO Juicer Directory: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__ 2021-09-13 07:02:22,546 INFO Juicer Genome assembly: mm10 2021-09-13 07:02:22,546 INFO Juicer Genome FASTA path: /Data/DataBases/mm10/mm10_canonic.fa 2021-09-13 07:02:22,546 INFO Juicer Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-13 07:02:22,546 INFO Juicer Enzyme: HindIII 2021-09-13 07:02:22,546 INFO Juicer Restriction sites path: /Data/UserData/FairWind/Ya.Cloud/core/pipeline/data/restriction_sites/RestrictionSites_HindIII_mm10.txt 2021-09-13 07:02:22,546 INFO Juicer Threads: 10 2021-09-13 07:02:22,546 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/HIC_tmp" 2021-09-13 07:02:22,599 INFO SimpleSubprocess RemoveTrash - 0:00:00 2021-09-13 07:02:22,599 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/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__" 2021-09-14 18:58:51,529 INFO SimpleSubprocess Juicer - 1 day, 11:56:28 2021-09-14 18:58:51,698 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/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__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/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits and /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned. bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129098_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129098_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129098.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129098.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129099_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129099_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129099.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129099.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129100_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129100_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129100.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129100.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129101_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129101_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129101.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129101.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129102_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129102_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129102.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129102.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129103_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129103_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129103.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129103.fastq.gz.sam done successfully bwa mem -SP5M -t 10 /Data/DataBases/mm10/mm10_canonic.fa /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129104_R1.fastq.gz /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129104_R2.fastq.gz > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129104.fastq.gz.sam (-: Align of /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/splits/SRR6129104.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 [2021-09-14T11:29:50,967] [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 [2021-09-14T15:41:23,154] [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/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__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 [2021-09-14T18:44:17,218] [Globals.java:138] [main] Development mode is enabled Reading file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_30.hic Using 1 CPU thread(s) Default settings for 10kb being used max 21.0 4% 9% 14% 19% 23% 28% 33% 38% 42% 47% 52% 57% 61% 66% 71% 76% 80% 85% 90% 95% 100% 843 features written to file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_30_contact_domains/10000_blocks.bedpe 843 domains written to file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_30_contact_domains/10000_blocks.bedpe Arrowhead complete 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/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned for results 2021-09-14 18:58:51,818 INFO MakeInterPairs Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/merged_nodups.txt 2021-09-14 18:58:51,818 INFO MakeInterPairs Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt 2021-09-14 18:58:51,870 DEBUG SimpleSubprocess awk -F " " '{print $2 "\t" $3 "\t" $6 "\t" $7}' "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/merged_nodups.txt" > "/tmp/tmpcbyl7hwl/inter.pairs.txt" 2021-09-14 19:09:02,531 INFO SimpleSubprocess MakeInterPairs - 0:10:10 2021-09-14 19:09:02,577 DEBUG SimpleSubprocess cp "/tmp/tmpcbyl7hwl/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt" 2021-09-14 19:09:27,906 INFO SimpleSubprocess CopyFiles - 0:00:25 2021-09-14 19:09:29,496 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt 2021-09-14 19:09:29,496 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-14 19:09:29,496 INFO Pairs2Cool Genome assembly: mm10 2021-09-14 19:09:29,497 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-14 19:09:29,497 INFO Pairs2Cool Resolution [bp]: 5000 2021-09-14 19:09:29,504 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/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt" "/tmp/tmpkhd678xl/inter_no_balanced.cool" 2021-09-14 19:19:59,283 INFO SimpleSubprocess MakeCool - 0:10:29 2021-09-14 19:19:59,283 DEBUG SimpleSubprocess cp "/tmp/tmpkhd678xl/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_5kb.cool" 2021-09-14 19:19:59,530 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-14 19:19:59,605 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt 2021-09-14 19:19:59,606 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-14 19:19:59,606 INFO Pairs2Cool Genome assembly: mm10 2021-09-14 19:19:59,606 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-14 19:19:59,606 INFO Pairs2Cool Resolution [bp]: 10000 2021-09-14 19:19:59,606 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/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt" "/tmp/tmp6h8g6j_i/inter_no_balanced.cool" 2021-09-14 19:29:34,716 INFO SimpleSubprocess MakeCool - 0:09:35 2021-09-14 19:29:34,717 DEBUG SimpleSubprocess cp "/tmp/tmp6h8g6j_i/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_10kb.cool" 2021-09-14 19:29:34,925 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-14 19:29:34,979 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt 2021-09-14 19:29:34,979 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-14 19:29:34,979 INFO Pairs2Cool Genome assembly: mm10 2021-09-14 19:29:34,979 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-14 19:29:34,979 INFO Pairs2Cool Resolution [bp]: 20000 2021-09-14 19:29:34,979 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/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt" "/tmp/tmpdp5_i840/inter_no_balanced.cool" 2021-09-14 19:38:26,822 INFO SimpleSubprocess MakeCool - 0:08:51 2021-09-14 19:38:26,822 DEBUG SimpleSubprocess cp "/tmp/tmpdp5_i840/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_20kb.cool" 2021-09-14 19:38:26,999 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-14 19:38:27,043 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt 2021-09-14 19:38:27,043 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-14 19:38:27,043 INFO Pairs2Cool Genome assembly: mm10 2021-09-14 19:38:27,043 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-14 19:38:27,043 INFO Pairs2Cool Resolution [bp]: 25000 2021-09-14 19:38:27,066 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/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt" "/tmp/tmp86lg3r42/inter_no_balanced.cool" 2021-09-14 19:47:07,644 INFO SimpleSubprocess MakeCool - 0:08:40 2021-09-14 19:47:07,644 DEBUG SimpleSubprocess cp "/tmp/tmp86lg3r42/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_25kb.cool" 2021-09-14 19:47:07,802 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-14 19:47:07,823 INFO Pairs2Cool Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt 2021-09-14 19:47:07,823 INFO Pairs2Cool Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-14 19:47:07,823 INFO Pairs2Cool Genome assembly: mm10 2021-09-14 19:47:07,824 INFO Pairs2Cool Chrom sizes file path: /Data/DataBases/mm10/mm10_canonic.chrom.sizes 2021-09-14 19:47:07,824 INFO Pairs2Cool Resolution [bp]: 50000 2021-09-14 19:47:07,824 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/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt" "/tmp/tmpyyvz2py0/inter_no_balanced.cool" 2021-09-14 19:55:12,875 INFO SimpleSubprocess MakeCool - 0:08:05 2021-09-14 19:55:12,875 DEBUG SimpleSubprocess cp "/tmp/tmpyyvz2py0/inter_no_balanced.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_50kb.cool" 2021-09-14 19:55:13,008 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-14 19:55:13,028 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_5kb.cool 2021-09-14 19:55:13,028 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_5kb.cool 2021-09-14 19:55:13,028 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-14 19:55:13,066 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_5kb.cool" "/tmp/tmpbnsvb9v7/inter.cool" 2021-09-14 19:55:13,332 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-14 19:55:13,333 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpbnsvb9v7/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-14 19:55:43,596 INFO SimpleSubprocess NormalizeCool - 0:00:30 2021-09-14 19:55:43,596 DEBUG SimpleSubprocess cp "/tmp/tmpbnsvb9v7/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_5kb.cool" 2021-09-14 19:55:43,840 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-14 19:55:43,873 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_10kb.cool 2021-09-14 19:55:43,874 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_10kb.cool 2021-09-14 19:55:43,874 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-14 19:55:43,895 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_10kb.cool" "/tmp/tmp56tq9z60/inter.cool" 2021-09-14 19:55:44,100 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-14 19:55:44,100 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmp56tq9z60/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-14 19:56:08,429 INFO SimpleSubprocess NormalizeCool - 0:00:24 2021-09-14 19:56:08,429 DEBUG SimpleSubprocess cp "/tmp/tmp56tq9z60/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_10kb.cool" 2021-09-14 19:56:08,646 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-14 19:56:08,677 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_20kb.cool 2021-09-14 19:56:08,677 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_20kb.cool 2021-09-14 19:56:08,677 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-14 19:56:08,677 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_20kb.cool" "/tmp/tmpfm2g9t70/inter.cool" 2021-09-14 19:56:08,864 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-14 19:56:08,864 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpfm2g9t70/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-14 19:56:13,029 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-09-14 19:56:13,029 DEBUG SimpleSubprocess cp "/tmp/tmpfm2g9t70/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_20kb.cool" 2021-09-14 19:56:13,212 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-14 19:56:13,263 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_25kb.cool 2021-09-14 19:56:13,263 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_25kb.cool 2021-09-14 19:56:13,263 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-14 19:56:13,263 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_25kb.cool" "/tmp/tmpor4aelwe/inter.cool" 2021-09-14 19:56:13,430 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-14 19:56:13,430 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmpor4aelwe/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-14 19:56:17,937 INFO SimpleSubprocess NormalizeCool - 0:00:04 2021-09-14 19:56:17,938 DEBUG SimpleSubprocess cp "/tmp/tmpor4aelwe/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_25kb.cool" 2021-09-14 19:56:18,101 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-14 19:56:18,143 INFO CTaleNormalize Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_50kb.cool 2021-09-14 19:56:18,143 INFO CTaleNormalize Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_50kb.cool 2021-09-14 19:56:18,143 INFO CTaleNormalize Capture: chrX:50,550,000-50,675,000 2021-09-14 19:56:18,143 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_50kb.cool" "/tmp/tmphh4na64u/inter.cool" 2021-09-14 19:56:18,277 INFO SimpleSubprocess TempFiles - 0:00:00 2021-09-14 19:56:18,277 DEBUG SimpleSubprocess ctale_normalize "/tmp/tmphh4na64u/inter.cool" "chrX:50,550,000-50,675,000" 2021-09-14 19:56:20,940 INFO SimpleSubprocess NormalizeCool - 0:00:02 2021-09-14 19:56:20,940 DEBUG SimpleSubprocess cp "/tmp/tmphh4na64u/inter.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_50kb.cool" 2021-09-14 19:56:21,061 INFO SimpleSubprocess CopyFiles - 0:00:00 2021-09-14 19:56:21,082 DEBUG SimpleSubprocess echo > /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/vector.txt 2021-09-14 19:56:21,088 INFO SimpleSubprocess MakeVector - 0:00:00 2021-09-14 19:56:21,115 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_5kb.cool 2021-09-14 19:56:21,115 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/vector.txt 2021-09-14 19:56:21,115 INFO AddWeight Chromosome: chrX 2021-09-14 19:56:21,115 INFO AddWeight Resolution [bp]: 5000 2021-09-14 19:56:22,196 INFO AddWeight AddWeight successfully finished 2021-09-14 19:56:22,196 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_10kb.cool 2021-09-14 19:56:22,196 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/vector.txt 2021-09-14 19:56:22,197 INFO AddWeight Chromosome: chrX 2021-09-14 19:56:22,197 INFO AddWeight Resolution [bp]: 10000 2021-09-14 19:56:22,248 INFO AddWeight AddWeight successfully finished 2021-09-14 19:56:22,248 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_20kb.cool 2021-09-14 19:56:22,248 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/vector.txt 2021-09-14 19:56:22,248 INFO AddWeight Chromosome: chrX 2021-09-14 19:56:22,248 INFO AddWeight Resolution [bp]: 20000 2021-09-14 19:56:22,294 INFO AddWeight AddWeight successfully finished 2021-09-14 19:56:22,295 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_25kb.cool 2021-09-14 19:56:22,295 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/vector.txt 2021-09-14 19:56:22,295 INFO AddWeight Chromosome: chrX 2021-09-14 19:56:22,295 INFO AddWeight Resolution [bp]: 25000 2021-09-14 19:56:22,335 INFO AddWeight AddWeight successfully finished 2021-09-14 19:56:22,335 INFO AddWeight Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_50kb.cool 2021-09-14 19:56:22,335 INFO AddWeight Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/vector.txt 2021-09-14 19:56:22,335 INFO AddWeight Chromosome: chrX 2021-09-14 19:56:22,335 INFO AddWeight Resolution [bp]: 50000 2021-09-14 19:56:22,358 INFO AddWeight AddWeight successfully finished 2021-09-14 19:56:22,368 INFO Vector2HiC Input file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.hic 2021-09-14 19:56:22,368 INFO Vector2HiC Output file: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_norm.hic 2021-09-14 19:56:22,368 INFO Vector2HiC Vector: /Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/vector.txt 2021-09-14 19:56:22,368 INFO Vector2HiC Threads: 10 2021-09-14 19:56:22,405 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.hic" "/tmp/tmp_cnll4dp/inter.hic" 2021-09-14 19:56:26,258 INFO SimpleSubprocess TempFiles - 0:00:03 2021-09-14 19:56:26,259 INFO Vector2HiC Vector: vector c-tale_normalization chrX 5000 BP 2021-09-14 19:56:26,294 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp_cnll4dp/inter.hic" "/tmp/tmp_cnll4dp/vector.txt" 2021-09-14 19:56:32,364 INFO SimpleSubprocess NormalizeHiC - 0:00:06 2021-09-14 19:56:32,365 INFO Vector2HiC Vector: vector c-tale_normalization chrX 10000 BP 2021-09-14 19:56:32,389 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp_cnll4dp/inter.hic" "/tmp/tmp_cnll4dp/vector.txt" 2021-09-14 19:56:36,825 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-14 19:56:36,825 INFO Vector2HiC Vector: vector c-tale_normalization chrX 20000 BP 2021-09-14 19:56:36,846 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp_cnll4dp/inter.hic" "/tmp/tmp_cnll4dp/vector.txt" 2021-09-14 19:56:40,786 INFO SimpleSubprocess NormalizeHiC - 0:00:03 2021-09-14 19:56:40,786 INFO Vector2HiC Vector: vector c-tale_normalization chrX 25000 BP 2021-09-14 19:56:40,827 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp_cnll4dp/inter.hic" "/tmp/tmp_cnll4dp/vector.txt" 2021-09-14 19:56:45,242 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-14 19:56:45,242 INFO Vector2HiC Vector: vector c-tale_normalization chrX 50000 BP 2021-09-14 19:56:45,293 DEBUG SimpleSubprocess java -jar "/Data/UserData/FairWind/Ya.Cloud/core/pipeline/scripts/../juicer/scripts/common/juicer_tools.jar" addNorm -j 10 "/tmp/tmp_cnll4dp/inter.hic" "/tmp/tmp_cnll4dp/vector.txt" 2021-09-14 19:56:49,569 INFO SimpleSubprocess NormalizeHiC - 0:00:04 2021-09-14 19:56:49,569 DEBUG SimpleSubprocess cp "/tmp/tmp_cnll4dp/inter.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_norm.hic" 2021-09-14 19:56:51,283 INFO SimpleSubprocess CopyFiles - 0:00:01 2021-09-14 19:56:51,828 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/merged_nodups.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/merged_nodups.txt" 2021-09-14 20:16:44,584 INFO SimpleSubprocess CopyResult - 0:19:52 2021-09-14 20:16:44,610 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.pairs.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter.pairs.txt" 2021-09-14 20:17:53,859 INFO SimpleSubprocess CopyResult - 0:01:09 2021-09-14 20:17:53,860 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/vector.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/vector.txt" 2021-09-14 20:17:53,884 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-14 20:17:53,884 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_norm.hic" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter.hic" 2021-09-14 20:18:14,628 INFO SimpleSubprocess CopyResult - 0:00:20 2021-09-14 20:18:14,628 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter.txt" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter_statistics.txt" 2021-09-14 20:18:14,679 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-14 20:18:14,680 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter_no_balanced_5kb.cool" 2021-09-14 20:18:18,017 INFO SimpleSubprocess CopyResult - 0:00:03 2021-09-14 20:18:18,018 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_5kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter_5kb.cool" 2021-09-14 20:18:19,963 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-14 20:18:19,963 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter_no_balanced_10kb.cool" 2021-09-14 20:18:21,732 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-14 20:18:21,733 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_10kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter_10kb.cool" 2021-09-14 20:18:24,263 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-14 20:18:24,263 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter_no_balanced_20kb.cool" 2021-09-14 20:18:25,812 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-14 20:18:25,812 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_20kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter_20kb.cool" 2021-09-14 20:18:27,846 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-14 20:18:27,846 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter_no_balanced_25kb.cool" 2021-09-14 20:18:30,710 INFO SimpleSubprocess CopyResult - 0:00:02 2021-09-14 20:18:30,710 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_25kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter_25kb.cool" 2021-09-14 20:18:32,606 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-14 20:18:32,606 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_no_balanced_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter_no_balanced_50kb.cool" 2021-09-14 20:18:33,582 INFO SimpleSubprocess CopyResult - 0:00:00 2021-09-14 20:18:33,582 DEBUG SimpleSubprocess cp "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__/aligned/inter_50kb.cool" "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/inter_50kb.cool" 2021-09-14 20:18:34,622 INFO SimpleSubprocess CopyResult - 0:00:01 2021-09-14 20:18:34,657 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__" 2021-09-14 20:19:19,533 INFO SimpleSubprocess RemoveTemp - 0:00:44 2021-09-14 20:19:19,552 INFO BenchmarkPipeline 'SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104' FINISHED, SUMMARY TIME - 1 day, 21:23:31 2021-09-20 11:27:07,144 INFO BenchmarkPipeline --- START PROCESSING 'SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104' --- 2021-09-20 11:27:07,155 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__" 2021-09-20 11:27:07,163 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-20 11:27:07,163 INFO BenchmarkPipeline 'SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104' FINISHED, SUMMARY TIME - 0:00:00 2021-09-20 11:28:38,882 INFO BenchmarkPipeline --- START PROCESSING 'SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104' --- 2021-09-20 11:28:38,882 DEBUG SimpleSubprocess rm -rf "/Data/NGS_Data/20210714_INC_COST_3DBenchmark/Project/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104/__temp__" 2021-09-20 11:28:38,890 INFO SimpleSubprocess RemoveTemp - 0:00:00 2021-09-20 11:28:38,890 INFO BenchmarkPipeline 'SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104' FINISHED, SUMMARY TIME - 0:00:00