RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.AjutgC/RM_13827.ThuMay110929472023 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: 1683822586 Database = /dev/shm/rModeler.AjutgC/GCA_027942885.1_fOdoBon6.hap2 - Sequences = 334 - Bases = 974945057 - N50 = 31128597 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 66190631-70917548 | [ 1 ] 61463714-66190630 | [ ] 56736797-61463713 | [ ] 52009881-56736797 | [ 1 ] 47282964-52009880 | [ 1 ] 42556047-47282963 | [ ] 37829130-42556046 | [ 3 ] 33102214-37829130 | [ 3 ] 28375297-33102213 | [ 6 ] 23648380-28375296 | [ 5 ] 18921463-23648379 | [ 2 ] 14194547-18921463 | [ ] 9467630-14194546 | [ ] 4740713-9467629 |* [ 11 ] 13797-4740713 |************************************************** [ 301 ] Storage Throughput = excellent ( 1142.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015739 bp ( 40011739 non ambiguous ) - Num Contigs Represented = 121 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:16 (hh:mm:ss) Elapsed Time Round Time: 00:32:06 (hh:mm:ss) Elapsed Time : 542 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7822 repeats masked totaling 2228359 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002898 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 10000898 bp After Masking: 6698479 bp Masked: 33.02 % -- Input Database Coverage: 10002898 bp out of 974945057 bp ( 1.03 % ) Sampling Time: 00:03:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:46 (hh:mm:ss) Elapsed Time, 5945 HSPs Collected Number of families returned by RECON: 1316 Round Time: 00:10:33 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22879 repeats masked totaling 6137549 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012816 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 30010816 bp After Masking: 20817232 bp Masked: 30.63 % -- Input Database Coverage: 40015714 bp out of 974945057 bp ( 4.10 % ) Sampling Time: 00:07:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:32:26 (hh:mm:ss) Elapsed Time, 46225 HSPs Collected Number of families returned by RECON: 4347 Round Time: 00:43:31 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 74833 repeats masked totaling 19765605 bp(s). - TE Masking time 00:02:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021926 bp Num Contigs Represented = 181 Non ambiguous bp: Initial: 90016926 bp After Masking: 60914681 bp Masked: 32.33 % -- Input Database Coverage: 130037640 bp out of 974945057 bp ( 13.34 % ) Sampling Time: 00:26:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 03:31:17 (hh:mm:ss) Elapsed Time, 365639 HSPs Collected Number of families returned by RECON: 13853 Round Time: 04:11:01 (hh:mm:ss) Elapsed Time : 465 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:57:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 289669 repeats masked totaling 77977296 bp(s). - TE Masking time 00:13:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022052 bp Num Contigs Represented = 249 Non ambiguous bp: Initial: 270003552 bp After Masking: 164662022 bp Masked: 39.01 % -- Input Database Coverage: 400059692 bp out of 974945057 bp ( 41.03 % ) Sampling Time: 01:15:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23082615 Comparison Time: 24:52:09 (hh:mm:ss) Elapsed Time, 1113001 HSPs Collected Number of families returned by RECON: 43874 Round Time: 27:27:42 (hh:mm:ss) Elapsed Time : 1198 families discovered. RepeatScout/RECON discovery complete: 2281 families found Classification Time: 02:33:11 (hh:mm:ss) Elapsed Time Program Time: 35:38:04 (hh:mm:ss) Elapsed Time