RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.n3evVo/RM_22625.ThuNov142332242024 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: 1731655943 Database = /scratch/tmp/rModeler.n3evVo/GCA_964188305.1_rPodBoc1.hap1.1 - Sequences = 507 - Bases = 1615206822 - N50 = 96534494 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 133157508-142668688 | [ 1 ] 123646329-133157508 | [ ] 114135150-123646329 | [ 1 ] 104623971-114135150 | [ 1 ] 95112792-104623971 | [ 4 ] 85601612-95112791 | [ 2 ] 76090433-85601612 | [ 2 ] 66579254-76090433 | [ ] 57068075-66579254 | [ 3 ] 47556896-57068075 | [ 2 ] 38045716-47556895 | [ 3 ] 28534537-38045716 | [ ] 19023358-28534537 | [ ] 9512179-19023358 | [ 1 ] 1000-9512179 |************************************************** [ 487 ] Storage Throughput = fair ( 356.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023450 bp ( 40019689 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:27 (hh:mm:ss) Elapsed Time Round Time: 00:34:11 (hh:mm:ss) Elapsed Time : 619 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18082 repeats masked totaling 3653462 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005099 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10005099 bp After Masking: 5988614 bp Masked: 40.14 % -- Input Database Coverage: 10005099 bp out of 1615206822 bp ( 0.62 % ) Sampling Time: 00:01:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:04:51 (hh:mm:ss) Elapsed Time, 7314 HSPs Collected Number of families returned by RECON: 1129 Round Time: 00:06:44 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56903 repeats masked totaling 11530259 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018271 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30014510 bp After Masking: 17574762 bp Masked: 41.45 % -- Input Database Coverage: 40023370 bp out of 1615206822 bp ( 2.48 % ) Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:24:07 (hh:mm:ss) Elapsed Time, 38590 HSPs Collected Number of families returned by RECON: 4000 Round Time: 00:30:25 (hh:mm:ss) Elapsed Time : 107 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 181719 repeats masked totaling 36119450 bp(s). - TE Masking time 00:02:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043240 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 90034240 bp After Masking: 51114372 bp Masked: 43.23 % -- Input Database Coverage: 130066610 bp out of 1615206822 bp ( 8.05 % ) Sampling Time: 00:12:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 02:41:43 (hh:mm:ss) Elapsed Time, 198073 HSPs Collected Number of families returned by RECON: 12632 Round Time: 03:06:47 (hh:mm:ss) Elapsed Time : 437 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 614411 repeats masked totaling 119319687 bp(s). - TE Masking time 00:11:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270070962 bp Num Contigs Represented = 168 Non ambiguous bp: Initial: 270034705 bp After Masking: 142002346 bp Masked: 47.41 % -- Input Database Coverage: 400137572 bp out of 1615206822 bp ( 24.77 % ) Sampling Time: 00:39:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 20:09:49 (hh:mm:ss) Elapsed Time, 511190 HSPs Collected Number of families returned by RECON: 42523 Round Time: 22:11:23 (hh:mm:ss) Elapsed Time : 1033 families discovered. RepeatScout/RECON discovery complete: 2219 families found Classification Time: 01:20:54 (hh:mm:ss) Elapsed Time Program Time: 27:50:24 (hh:mm:ss) Elapsed Time