RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.1MGy1x/RM_3869279.ThuMar140938282024 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: 1710434307 Database = /dev/shm/rModeler.1MGy1x/GCA_035149785.1_rCanAsp1.hap2 - Sequences = 150 - Bases = 1530827941 - N50 = 265922563 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 321060903-343993754 | [ 1 ] 298128053-321060903 | [ ] 275195203-298128053 | [ ] 252262352-275195202 | [ 1 ] 229329502-252262352 | [ ] 206396652-229329502 | [ 1 ] 183463802-206396652 | [ ] 160530951-183463801 | [ ] 137598101-160530951 | [ ] 114665251-137598101 | [ 2 ] 91732401-114665251 | [ 1 ] 68799550-91732400 | [ 2 ] 45866700-68799550 | [ ] 22933850-45866700 |* [ 5 ] 1000-22933850 |************************************************* [ 137 ] Storage Throughput = excellent ( 1343.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027458 bp ( 40026858 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:03:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:02 (hh:mm:ss) Elapsed Time Round Time: 00:24:10 (hh:mm:ss) Elapsed Time : 359 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9467 repeats masked totaling 2925371 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000165 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10000165 bp After Masking: 7002556 bp Masked: 29.98 % -- Input Database Coverage: 10000165 bp out of 1530827941 bp ( 0.65 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:09:10 (hh:mm:ss) Elapsed Time, 9631 HSPs Collected Number of families returned by RECON: 1286 Round Time: 00:11:25 (hh:mm:ss) Elapsed Time : 32 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32311 repeats masked totaling 9040645 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027213 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30026613 bp After Masking: 20493906 bp Masked: 31.75 % -- Input Database Coverage: 40027378 bp out of 1530827941 bp ( 2.61 % ) Sampling Time: 00:04:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:34:39 (hh:mm:ss) Elapsed Time, 30288 HSPs Collected Number of families returned by RECON: 3722 Round Time: 00:40:06 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109497 repeats masked totaling 29285334 bp(s). - TE Masking time 00:01:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032408 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 90030408 bp After Masking: 59585221 bp Masked: 33.82 % -- Input Database Coverage: 130059786 bp out of 1530827941 bp ( 8.50 % ) Sampling Time: 00:13:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 02:56:08 (hh:mm:ss) Elapsed Time, 172504 HSPs Collected Number of families returned by RECON: 12797 Round Time: 03:16:18 (hh:mm:ss) Elapsed Time : 325 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:24:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 383304 repeats masked totaling 99124850 bp(s). - TE Masking time 00:06:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270013479 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 270010079 bp After Masking: 166379170 bp Masked: 38.38 % -- Input Database Coverage: 400073265 bp out of 1530827941 bp ( 26.13 % ) Sampling Time: 00:40:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 20:25:46 (hh:mm:ss) Elapsed Time, 421274 HSPs Collected Number of families returned by RECON: 46167 Round Time: 21:49:15 (hh:mm:ss) Elapsed Time : 791 families discovered. RepeatScout/RECON discovery complete: 1589 families found Classification Time: 00:56:52 (hh:mm:ss) Elapsed Time Program Time: 27:18:06 (hh:mm:ss) Elapsed Time