RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.nuajdO/RM_294385.FriFeb71211482025 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: 1738959100 Database = /data/tmp/rModeler.nuajdO/GCA_045364805.1_bWilVid1_haplotype_2 - Sequences = 743 - Bases = 1070918723 - N50 = 78239105 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 116376873-124689436 | [ 2 ] 108064311-116376873 | [ ] 99751748-108064310 | [ 1 ] 91439186-99751748 | [ ] 83126624-91439186 | [ ] 74814061-83126623 | [ 2 ] 66501499-74814061 | [ 1 ] 58188936-66501498 | [ 1 ] 49876374-58188936 | [ 2 ] 41563812-49876374 | [ ] 33251249-41563811 | [ ] 24938687-33251249 | [ 2 ] 16626124-24938686 | [ 6 ] 8313562-16626124 | [ 3 ] 1000-8313562 |************************************************** [ 723 ] Storage Throughput = excellent ( 1704.58 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039719 bp ( 40034719 non ambiguous ) - Num Contigs Represented = 95 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:17 (hh:mm:ss) Elapsed Time Round Time: 00:12:41 (hh:mm:ss) Elapsed Time : 129 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (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... 3044 repeats masked totaling 822564 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029994 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10028994 bp After Masking: 8763439 bp Masked: 12.62 % -- Input Database Coverage: 10029994 bp out of 1070918723 bp ( 0.94 % ) Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 704 HSPs Collected Number of families returned by RECON: 232 Round Time: 00:03:46 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9098 repeats masked totaling 2605429 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009645 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 30005645 bp After Masking: 25949391 bp Masked: 13.52 % -- Input Database Coverage: 40039639 bp out of 1070918723 bp ( 3.74 % ) Sampling Time: 00:02:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296065 Comparison Time: 00:15:48 (hh:mm:ss) Elapsed Time, 4708 HSPs Collected Number of families returned by RECON: 1491 Round Time: 00:18:16 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27765 repeats masked totaling 7721810 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032168 bp Num Contigs Represented = 137 Non ambiguous bp: Initial: 90023768 bp After Masking: 77811863 bp Masked: 13.57 % -- Input Database Coverage: 130071807 bp out of 1070918723 bp ( 12.15 % ) Sampling Time: 00:05:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2602621 Comparison Time: 01:51:34 (hh:mm:ss) Elapsed Time, 41797 HSPs Collected Number of families returned by RECON: 10416 Round Time: 01:59:57 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 89724 repeats masked totaling 25380134 bp(s). - TE Masking time 00:01:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041111 bp Num Contigs Represented = 289 Non ambiguous bp: Initial: 270012887 bp After Masking: 230899261 bp Masked: 14.49 % -- Input Database Coverage: 400112918 bp out of 1070918723 bp ( 37.36 % ) Sampling Time: 00:18:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23396220 Comparison Time: 16:24:05 (hh:mm:ss) Elapsed Time, 215273 HSPs Collected Number of families returned by RECON: 68866 Round Time: 17:12:50 (hh:mm:ss) Elapsed Time : 279 families discovered. RepeatScout/RECON discovery complete: 483 families found Classification Time: 00:19:43 (hh:mm:ss) Elapsed Time Program Time: 20:07:13 (hh:mm:ss) Elapsed Time