RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KgNAPC/RM_2451444.MonJul152153552024 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: 1721105634 Database = /dev/shm/rModeler.KgNAPC/GCF_024868665.1_Trosa_1v2 - Sequences = 1039 - Bases = 684821613 - N50 = 25840106 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 37455664-40131052 | [ 1 ] 34780276-37455663 | [ 1 ] 32104888-34780275 | [ 1 ] 29429500-32104887 | [ 1 ] 26754113-29429500 | [ 6 ] 24078725-26754112 | [ 3 ] 21403337-24078724 | [ 6 ] 18727949-21403336 | [ 3 ] 16052561-18727948 | [ 2 ] 13377174-16052561 | [ 1 ] 10701786-13377173 | [ ] 8026398-10701785 | [ ] 5351010-8026397 | [ ] 2675622-5351009 | [ ] 235-2675622 |************************************************** [ 1014 ] Storage Throughput = excellent ( 1321.32 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40623258 bp ( 40006687 non ambiguous ) - Num Contigs Represented = 146 - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:52 (hh:mm:ss) Elapsed Time Round Time: 00:23:59 (hh:mm:ss) Elapsed Time : 915 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 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13530 repeats masked totaling 3116375 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10198091 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 10007659 bp After Masking: 6739108 bp Masked: 32.66 % -- Input Database Coverage: 10198091 bp out of 684821613 bp ( 1.49 % ) Sampling Time: 00:01:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34980 Comparison Time: 00:08:43 (hh:mm:ss) Elapsed Time, 12557 HSPs Collected Number of families returned by RECON: 1276 Round Time: 00:10:19 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41951 repeats masked totaling 9586679 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30465090 bp Num Contigs Represented = 119 Non ambiguous bp: Initial: 30038851 bp After Masking: 20066026 bp Masked: 33.20 % -- Input Database Coverage: 40663181 bp out of 684821613 bp ( 5.94 % ) Sampling Time: 00:02:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 316410 Comparison Time: 00:45:31 (hh:mm:ss) Elapsed Time, 38620 HSPs Collected Number of families returned by RECON: 4189 Round Time: 00:50:14 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 131772 repeats masked totaling 29654131 bp(s). - TE Masking time 00:02:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91519741 bp Num Contigs Represented = 256 Non ambiguous bp: Initial: 90015665 bp After Masking: 59215715 bp Masked: 34.22 % -- Input Database Coverage: 132182922 bp out of 684821613 bp ( 19.30 % ) Sampling Time: 00:08:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2823876 Comparison Time: 03:38:54 (hh:mm:ss) Elapsed Time, 289385 HSPs Collected Number of families returned by RECON: 13427 Round Time: 03:58:40 (hh:mm:ss) Elapsed Time : 594 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 463708 repeats masked totaling 104549360 bp(s). - TE Masking time 00:12:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273680296 bp Num Contigs Represented = 608 Non ambiguous bp: Initial: 270037830 bp After Masking: 161917114 bp Masked: 40.04 % -- Input Database Coverage: 405863218 bp out of 684821613 bp ( 59.27 % ) Sampling Time: 00:29:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25550526 Comparison Time: 30:59:19 (hh:mm:ss) Elapsed Time, 712150 HSPs Collected Number of families returned by RECON: 43653 Round Time: 32:35:07 (hh:mm:ss) Elapsed Time : 1151 families discovered. RepeatScout/RECON discovery complete: 2755 families found Classification Time: 01:52:34 (hh:mm:ss) Elapsed Time Program Time: 39:50:53 (hh:mm:ss) Elapsed Time