RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.33en1M/RM_53415.MonJan21258462023 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: 1672693126 Database = /dev/shm/rModeler.33en1M/GCF_900246225.1_fAstCal1.2 - Sequences = 249 - Bases = 880445564 - N50 = 38678279 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 63839031-68397778 | [ 1 ] 59280284-63839030 | [ ] 54721538-59280284 | [ ] 50162791-54721537 | [ 1 ] 45604044-50162790 | [ ] 41045298-45604044 | [ 3 ] 36486551-41045297 |* [ 7 ] 31927804-36486550 |* [ 7 ] 27369058-31927804 | [ 2 ] 22810311-27369057 | [ 1 ] 18251564-22810310 | [ ] 13692818-18251564 | [ ] 9134071-13692817 | [ ] 4575324-9134070 | [ ] 16578-4575324 |************************************************** [ 227 ] Storage Throughput = excellent ( 1366.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40094894 bp ( 40029200 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:50 (hh:mm:ss) Elapsed Time Round Time: 00:19:13 (hh:mm:ss) Elapsed Time : 600 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9410 repeats masked totaling 2358083 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005349 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10004974 bp After Masking: 7505433 bp Masked: 24.98 % -- Input Database Coverage: 10005349 bp out of 880445564 bp ( 1.14 % ) Sampling Time: 00:00:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:20 (hh:mm:ss) Elapsed Time, 7522 HSPs Collected Number of families returned by RECON: 1269 Round Time: 00:06:23 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29723 repeats masked totaling 7338761 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30089543 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30024224 bp After Masking: 22343330 bp Masked: 25.58 % -- Input Database Coverage: 40094892 bp out of 880445564 bp ( 4.55 % ) Sampling Time: 00:02:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:26:28 (hh:mm:ss) Elapsed Time, 41343 HSPs Collected Number of families returned by RECON: 4364 Round Time: 00:30:09 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100780 repeats masked totaling 24209000 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90124944 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 90035288 bp After Masking: 64716331 bp Masked: 28.12 % -- Input Database Coverage: 130219836 bp out of 880445564 bp ( 14.79 % ) Sampling Time: 00:07:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 02:57:39 (hh:mm:ss) Elapsed Time, 224880 HSPs Collected Number of families returned by RECON: 14288 Round Time: 03:15:14 (hh:mm:ss) Elapsed Time : 397 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 353585 repeats masked totaling 84762284 bp(s). - TE Masking time 00:11:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270566592 bp Num Contigs Represented = 139 Non ambiguous bp: Initial: 270027066 bp After Masking: 182016220 bp Masked: 32.59 % -- Input Database Coverage: 400786428 bp out of 880445564 bp ( 45.52 % ) Sampling Time: 00:31:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23089410 Comparison Time: 22:47:50 (hh:mm:ss) Elapsed Time, 628617 HSPs Collected Number of families returned by RECON: 53440 Round Time: 24:34:15 (hh:mm:ss) Elapsed Time : 1035 families discovered. RepeatScout/RECON discovery complete: 2139 families found Classification Time: 02:03:25 (hh:mm:ss) Elapsed Time Program Time: 30:48:39 (hh:mm:ss) Elapsed Time