RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.PwkjLD/RM_3098456.FriAug10212312025 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: 1754039550 Database = /dev/shm/rModeler.PwkjLD/GCA_014338405.1_P_miyazaki_1.0.pg.lrna - Sequences = 22318 - Bases = 915809684 - N50 = 108807 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 858577-919833 | [ 1 ] 797321-858576 | [ 1 ] 736066-797321 | [ ] 674810-736065 | [ 3 ] 613555-674810 | [ 5 ] 552299-613554 | [ 15 ] 491044-552299 | [ 19 ] 429788-491043 | [ 33 ] 368533-429788 | [ 56 ] 307277-368532 | [ 133 ] 246022-307277 | [ 222 ] 184766-246021 |* [ 463 ] 123511-184766 |** [ 978 ] 62255-123510 |******* [ 2606 ] 1000-62255 |************************************************** [ 17783 ] Storage Throughput = excellent ( 1680.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43807065 bp ( 40024454 non ambiguous ) - Num Contigs Represented = 1693 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:04:34 (hh:mm:ss) Elapsed Time Round Time: 00:07:06 (hh:mm:ss) Elapsed Time : 633 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13401 repeats masked totaling 4389591 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11013170 bp Num Contigs Represented = 421 Non ambiguous bp: Initial: 10014360 bp After Masking: 5613723 bp Masked: 43.94 % -- Input Database Coverage: 11013170 bp out of 915809684 bp ( 1.20 % ) Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 91806 Comparison Time: 00:03:22 (hh:mm:ss) Elapsed Time, 3435 HSPs Collected Number of families returned by RECON: 656 Round Time: 00:03:39 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41299 repeats masked totaling 13678364 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32793843 bp Num Contigs Represented = 1309 Non ambiguous bp: Initial: 30010042 bp After Masking: 16294439 bp Masked: 45.70 % -- Input Database Coverage: 43807013 bp out of 915809684 bp ( 4.78 % ) Sampling Time: 00:00:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 914628 Comparison Time: 00:13:08 (hh:mm:ss) Elapsed Time, 26395 HSPs Collected Number of families returned by RECON: 2268 Round Time: 00:14:06 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 132722 repeats masked totaling 43635898 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 98392889 bp Num Contigs Represented = 3657 Non ambiguous bp: Initial: 90035488 bp After Masking: 46289537 bp Masked: 48.59 % -- Input Database Coverage: 142199902 bp out of 915809684 bp ( 15.53 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 8195176 Comparison Time: 01:03:02 (hh:mm:ss) Elapsed Time, 101310 HSPs Collected Number of families returned by RECON: 7050 Round Time: 01:06:11 (hh:mm:ss) Elapsed Time : 273 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 437366 repeats masked totaling 142643799 bp(s). - TE Masking time 00:02:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 295779959 bp Num Contigs Represented = 9522 Non ambiguous bp: Initial: 270024291 bp After Masking: 127085397 bp Masked: 52.94 % -- Input Database Coverage: 437979861 bp out of 915809684 bp ( 47.82 % ) Sampling Time: 00:05:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 75675753 Comparison Time: 06:24:10 (hh:mm:ss) Elapsed Time, 245084 HSPs Collected Number of families returned by RECON: 23913 Round Time: 06:36:38 (hh:mm:ss) Elapsed Time : 554 families discovered. RepeatScout/RECON discovery complete: 1533 families found Classification Time: 00:33:33 (hh:mm:ss) Elapsed Time Program Time: 08:41:13 (hh:mm:ss) Elapsed Time