RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.NbP0cH/RM_2904732.WedMar270422172024 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: 1711538537 Database = /dev/shm/rModeler.NbP0cH/GCA_963691925.1_fScoSco1.1 - Sequences = 666 - Bases = 764157853 - N50 = 31899851 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 36171244-38754833 | [ 2 ] 33587655-36171243 | [ 4 ] 31004066-33587654 | [ 6 ] 28420477-31004065 | [ 7 ] 25836888-28420476 | [ ] 23253299-25836887 | [ 4 ] 20669710-23253298 | [ ] 18086122-20669710 | [ ] 15502533-18086121 | [ 1 ] 12918944-15502532 | [ ] 10335355-12918943 | [ ] 7751766-10335354 | [ ] 5168177-7751765 | [ ] 2584588-5168176 | [ ] 1000-2584588 |************************************************** [ 642 ] Storage Throughput = excellent ( 1425.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031360 bp ( 40016360 non ambiguous ) - Num Contigs Represented = 88 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:54 (hh:mm:ss) Elapsed Time Round Time: 00:23:18 (hh:mm:ss) Elapsed Time : 423 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6977 repeats masked totaling 968860 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10042421 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10037821 bp After Masking: 8209174 bp Masked: 18.22 % -- Input Database Coverage: 10042421 bp out of 764157853 bp ( 1.31 % ) Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33670 Comparison Time: 00:06:31 (hh:mm:ss) Elapsed Time, 8853 HSPs Collected Number of families returned by RECON: 1662 Round Time: 00:08:22 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22299 repeats masked totaling 3053146 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028859 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30018459 bp After Masking: 24828053 bp Masked: 17.29 % -- Input Database Coverage: 40071280 bp out of 764157853 bp ( 5.24 % ) Sampling Time: 00:04:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 298378 Comparison Time: 00:32:51 (hh:mm:ss) Elapsed Time, 58960 HSPs Collected Number of families returned by RECON: 6375 Round Time: 00:38:48 (hh:mm:ss) Elapsed Time : 135 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 76780 repeats masked totaling 10974609 bp(s). - TE Masking time 00:01:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044814 bp Num Contigs Represented = 134 Non ambiguous bp: Initial: 90010465 bp After Masking: 72225601 bp Masked: 19.76 % -- Input Database Coverage: 130116094 bp out of 764157853 bp ( 17.03 % ) Sampling Time: 00:13:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2623195 Comparison Time: 03:22:13 (hh:mm:ss) Elapsed Time, 330584 HSPs Collected Number of families returned by RECON: 21067 Round Time: 03:49:33 (hh:mm:ss) Elapsed Time : 500 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 299307 repeats masked totaling 46505093 bp(s). - TE Masking time 00:07:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270140767 bp Num Contigs Represented = 326 Non ambiguous bp: Initial: 270032041 bp After Masking: 202371332 bp Masked: 25.06 % -- Input Database Coverage: 400256861 bp out of 764157853 bp ( 52.38 % ) Sampling Time: 00:45:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23773960 Comparison Time: 26:14:39 (hh:mm:ss) Elapsed Time, 970725 HSPs Collected Number of families returned by RECON: 74114 Round Time: 28:51:19 (hh:mm:ss) Elapsed Time : 1463 families discovered. RepeatScout/RECON discovery complete: 2541 families found Classification Time: 01:37:26 (hh:mm:ss) Elapsed Time Program Time: 35:28:46 (hh:mm:ss) Elapsed Time