RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.bYYPRo/RM_14930.SatMay131722322023 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: 1684023751 Database = /dev/shm/rModeler.bYYPRo/GCA_900700375.2_fDenClu1.2 - Sequences = 461 - Bases = 567417970 - N50 = 23378448 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 39360639-42171479 | [ 1 ] 36549799-39360638 | [ 2 ] 33738959-36549798 | [ 2 ] 30928119-33738958 | [ ] 28117280-30928119 | [ ] 25306440-28117279 | [ 2 ] 22495600-25306439 | [ 5 ] 19684760-22495599 | [ 7 ] 16873920-19684759 | [ 1 ] 14063081-16873920 | [ ] 11252241-14063080 | [ ] 8441401-11252240 | [ ] 5630561-8441400 | [ ] 2819721-5630560 | [ ] 8882-2819721 |************************************************** [ 441 ] Storage Throughput = excellent ( 1075.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40228169 bp ( 40037432 non ambiguous ) - Num Contigs Represented = 116 - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:02 (hh:mm:ss) Elapsed Time Round Time: 00:23:32 (hh:mm:ss) Elapsed Time : 474 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11450 repeats masked totaling 1717183 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019287 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10019287 bp After Masking: 8049184 bp Masked: 19.66 % -- Input Database Coverage: 10019287 bp out of 567417970 bp ( 1.77 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:06:46 (hh:mm:ss) Elapsed Time, 6295 HSPs Collected Number of families returned by RECON: 1259 Round Time: 00:07:54 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34058 repeats masked totaling 5289127 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30208802 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 30018065 bp After Masking: 23858245 bp Masked: 20.52 % -- Input Database Coverage: 40228089 bp out of 567417970 bp ( 7.09 % ) Sampling Time: 00:02:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 00:35:56 (hh:mm:ss) Elapsed Time, 81375 HSPs Collected Number of families returned by RECON: 4760 Round Time: 00:40:07 (hh:mm:ss) Elapsed Time : 116 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111715 repeats masked totaling 17350701 bp(s). - TE Masking time 00:01:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90896616 bp Num Contigs Represented = 180 Non ambiguous bp: Initial: 90005653 bp After Masking: 69993625 bp Masked: 22.23 % -- Input Database Coverage: 131124705 bp out of 567417970 bp ( 23.11 % ) Sampling Time: 00:07:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2648451 Comparison Time: 04:04:47 (hh:mm:ss) Elapsed Time, 301481 HSPs Collected Number of families returned by RECON: 16241 Round Time: 04:24:26 (hh:mm:ss) Elapsed Time : 348 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 406671 repeats masked totaling 63149946 bp(s). - TE Masking time 00:09:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272416894 bp Num Contigs Represented = 349 Non ambiguous bp: Initial: 270021394 bp After Masking: 199379994 bp Masked: 26.16 % -- Input Database Coverage: 403541599 bp out of 567417970 bp ( 71.12 % ) Sampling Time: 00:26:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23967426 Comparison Time: 31:18:36 (hh:mm:ss) Elapsed Time, 1625970 HSPs Collected Number of families returned by RECON: 63050 Round Time: 33:28:28 (hh:mm:ss) Elapsed Time : 796 families discovered. RepeatScout/RECON discovery complete: 1747 families found Classification Time: 01:38:09 (hh:mm:ss) Elapsed Time Program Time: 40:42:36 (hh:mm:ss) Elapsed Time