RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.cAxP9S/RM_1094967.WedNov130637022024 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: 1731508622 Database = /scratch/tmp/rModeler.cAxP9S/GCA_038363145.1_mArtInt1.hap1 - Sequences = 419 - Bases = 2293600955 - N50 = 176201619 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 229047550-245407277 | [ 1 ] 212687824-229047550 | [ 1 ] 196328098-212687824 | [ ] 179968372-196328098 | [ 2 ] 163608646-179968372 | [ 1 ] 147248920-163608646 | [ 3 ] 130889194-147248920 | [ 2 ] 114529468-130889194 | [ 1 ] 98169742-114529468 | [ 2 ] 81810016-98169742 | [ ] 65450290-81810016 | [ ] 49090564-65450290 | [ 2 ] 32730838-49090564 | [ 1 ] 16371112-32730838 | [ 1 ] 11386-16371112 |************************************************** [ 402 ] Storage Throughput = excellent ( 1458.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011985 bp ( 40011785 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:11 (hh:mm:ss) Elapsed Time Round Time: 00:12:59 (hh:mm:ss) Elapsed Time : 236 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9069 repeats masked totaling 2455036 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025789 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10025789 bp After Masking: 7431455 bp Masked: 25.88 % -- Input Database Coverage: 10025789 bp out of 2293600955 bp ( 0.44 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:09 (hh:mm:ss) Elapsed Time, 46114 HSPs Collected Number of families returned by RECON: 748 Round Time: 00:03:58 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31600 repeats masked totaling 8288114 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026195 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30025995 bp After Masking: 21506494 bp Masked: 28.37 % -- Input Database Coverage: 40051984 bp out of 2293600955 bp ( 1.75 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:59 (hh:mm:ss) Elapsed Time, 192179 HSPs Collected Number of families returned by RECON: 2419 Round Time: 00:15:38 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104741 repeats masked totaling 26996716 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029580 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90029480 bp After Masking: 61785544 bp Masked: 31.37 % -- Input Database Coverage: 130081564 bp out of 2293600955 bp ( 5.67 % ) Sampling Time: 00:05:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 01:20:20 (hh:mm:ss) Elapsed Time, 2207125 HSPs Collected Number of families returned by RECON: 7057 Round Time: 01:27:58 (hh:mm:ss) Elapsed Time : 157 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 331284 repeats masked totaling 84907123 bp(s). - TE Masking time 00:01:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270040585 bp Num Contigs Represented = 96 Non ambiguous bp: Initial: 270039185 bp After Masking: 181024388 bp Masked: 32.96 % -- Input Database Coverage: 400122149 bp out of 2293600955 bp ( 17.45 % ) Sampling Time: 00:18:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22974031 Comparison Time: 10:52:45 (hh:mm:ss) Elapsed Time, 34180538 HSPs Collected Number of families returned by RECON: 32976 Round Time: 11:28:25 (hh:mm:ss) Elapsed Time : 400 families discovered. RepeatScout/RECON discovery complete: 884 families found Classification Time: 00:21:06 (hh:mm:ss) Elapsed Time Program Time: 13:50:04 (hh:mm:ss) Elapsed Time