RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.42f6lT/RM_2006121.MonApr140102242025 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: 1744617743 Database = /data/tmp/rModeler.42f6lT/GCA_044231675.1_ASM4423167v1 - Sequences = 300 - Bases = 492062741 - N50 = 23778664 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 33786497-36199747 | [ 1 ] 31373247-33786496 | [ 2 ] 28959997-31373246 | [ 2 ] 26546747-28959996 | [ ] 24133498-26546747 | [ 2 ] 21720248-24133497 |* [ 6 ] 19306998-21720247 | [ 2 ] 16893748-19306997 | [ 1 ] 14480498-16893747 | [ 4 ] 12067249-14480498 | [ ] 9653999-12067248 | [ ] 7240749-9653998 | [ ] 4827499-7240748 | [ ] 2414249-4827498 | [ ] 1000-2414249 |************************************************** [ 280 ] Storage Throughput = good ( 854.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039475 bp ( 40038775 non ambiguous ) - Num Contigs Represented = 72 - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:44 (hh:mm:ss) Elapsed Time Round Time: 00:20:46 (hh:mm:ss) Elapsed Time : 336 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5958 repeats masked totaling 839592 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026406 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10026306 bp After Masking: 8600964 bp Masked: 14.22 % -- Input Database Coverage: 10026406 bp out of 492062741 bp ( 2.04 % ) Sampling Time: 00:02:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:16 (hh:mm:ss) Elapsed Time, 6299 HSPs Collected Number of families returned by RECON: 1094 Round Time: 00:08:58 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18664 repeats masked totaling 2768883 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012989 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30012389 bp After Masking: 25557519 bp Masked: 14.84 % -- Input Database Coverage: 40039395 bp out of 492062741 bp ( 8.14 % ) Sampling Time: 00:09:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:28:40 (hh:mm:ss) Elapsed Time, 38812 HSPs Collected Number of families returned by RECON: 4516 Round Time: 00:42:28 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67793 repeats masked totaling 10056305 bp(s). - TE Masking time 00:01:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030999 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 90028699 bp After Masking: 74767768 bp Masked: 16.95 % -- Input Database Coverage: 130070394 bp out of 492062741 bp ( 26.43 % ) Sampling Time: 00:20:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2595781 Comparison Time: 03:15:28 (hh:mm:ss) Elapsed Time, 185360 HSPs Collected Number of families returned by RECON: 15964 Round Time: 04:05:00 (hh:mm:ss) Elapsed Time : 293 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 248539 repeats masked totaling 39053602 bp(s). - TE Masking time 00:05:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270010020 bp Num Contigs Represented = 224 Non ambiguous bp: Initial: 270004620 bp After Masking: 215733499 bp Masked: 20.10 % -- Input Database Coverage: 400080414 bp out of 492062741 bp ( 81.31 % ) Sampling Time: 01:10:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23375703 Comparison Time: 23:03:49 (hh:mm:ss) Elapsed Time, 604743 HSPs Collected Number of families returned by RECON: 66767 Round Time: 27:21:18 (hh:mm:ss) Elapsed Time : 791 families discovered. RepeatScout/RECON discovery complete: 1545 families found Classification Time: 01:02:50 (hh:mm:ss) Elapsed Time Program Time: 33:41:20 (hh:mm:ss) Elapsed Time