RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5LvrVC/RM_400910.SatDec21204562023 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1701547494 Database = /dev/shm/rModeler.5LvrVC/GCF_026419965.1_mKogBre1_haplotype_1 - Sequences = 581 - Bases = 2555855246 - N50 = 139403296 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 188928309-202422507 | [ 2 ] 175434112-188928309 | [ 2 ] 161939914-175434111 | [ ] 148445717-161939914 | [ 1 ] 134951519-148445716 | [ 2 ] 121457322-134951519 | [ 1 ] 107963124-121457321 | [ 2 ] 94468927-107963124 | [ 3 ] 80974729-94468926 | [ 3 ] 67480532-80974729 | [ 2 ] 53986334-67480531 | [ 2 ] 40492137-53986334 | [ 1 ] 26997939-40492136 | [ ] 13503742-26997939 | [ ] 9545-13503742 |************************************************** [ 560 ] Storage Throughput = excellent ( 1185.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40109505 bp ( 40029292 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:50 (hh:mm:ss) Elapsed Time Round Time: 00:24:13 (hh:mm:ss) Elapsed Time : 231 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12686 repeats masked totaling 3145722 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021925 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10021912 bp After Masking: 6610221 bp Masked: 34.04 % -- Input Database Coverage: 10021925 bp out of 2555855246 bp ( 0.39 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:00 (hh:mm:ss) Elapsed Time, 8383 HSPs Collected Number of families returned by RECON: 842 Round Time: 00:07:18 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39843 repeats masked totaling 10152748 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30087500 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30007300 bp After Masking: 19434495 bp Masked: 35.23 % -- Input Database Coverage: 40109425 bp out of 2555855246 bp ( 1.57 % ) Sampling Time: 00:03:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:26:17 (hh:mm:ss) Elapsed Time, 34691 HSPs Collected Number of families returned by RECON: 2293 Round Time: 00:30:27 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 126461 repeats masked totaling 31998653 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90230850 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 90037126 bp After Masking: 56657906 bp Masked: 37.07 % -- Input Database Coverage: 130340275 bp out of 2555855246 bp ( 5.10 % ) Sampling Time: 00:10:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 02:09:27 (hh:mm:ss) Elapsed Time, 121341 HSPs Collected Number of families returned by RECON: 8149 Round Time: 02:25:41 (hh:mm:ss) Elapsed Time : 164 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 413276 repeats masked totaling 105951749 bp(s). - TE Masking time 00:03:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270654690 bp Num Contigs Represented = 160 Non ambiguous bp: Initial: 270018132 bp After Masking: 159223833 bp Masked: 41.03 % -- Input Database Coverage: 400994965 bp out of 2555855246 bp ( 15.69 % ) Sampling Time: 00:31:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23109801 Comparison Time: 14:45:58 (hh:mm:ss) Elapsed Time, 703878 HSPs Collected Number of families returned by RECON: 32761 Round Time: 15:47:52 (hh:mm:ss) Elapsed Time : 373 families discovered. RepeatScout/RECON discovery complete: 841 families found Classification Time: 00:28:35 (hh:mm:ss) Elapsed Time Program Time: 19:44:06 (hh:mm:ss) Elapsed Time