RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.gmmoe8/RM_933177.WedNov130636042024 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: 1731508561 Database = /scratch/tmp/rModeler.gmmoe8/GCA_964030765.1_fMicPou1.1 - Sequences = 3832 - Bases = 520636573 - N50 = 20052117 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 28402421-30431094 | [ 1 ] 26373748-28402420 | [ ] 24345075-26373747 | [ ] 22316402-24345074 | [ 5 ] 20287729-22316401 | [ 4 ] 18259056-20287728 | [ 6 ] 16230383-18259055 | [ 1 ] 14201710-16230382 | [ 5 ] 12173037-14201709 | [ ] 10144364-12173036 | [ 1 ] 8115691-10144363 | [ ] 6087018-8115690 | [ 1 ] 4058345-6087017 | [ ] 2029672-4058344 | [ ] 1000-2029672 |************************************************** [ 3808 ] Storage Throughput = excellent ( 1505.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40064558 bp ( 40018274 non ambiguous ) - Num Contigs Represented = 335 - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:49 (hh:mm:ss) Elapsed Time Round Time: 00:12:23 (hh:mm:ss) Elapsed Time : 472 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6006 repeats masked totaling 1014464 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019531 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 10005931 bp After Masking: 7671867 bp Masked: 23.33 % -- Input Database Coverage: 10019531 bp out of 520636573 bp ( 1.92 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 43660 Comparison Time: 00:03:18 (hh:mm:ss) Elapsed Time, 4369 HSPs Collected Number of families returned by RECON: 1122 Round Time: 00:04:32 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17442 repeats masked totaling 3225562 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30044947 bp Num Contigs Represented = 267 Non ambiguous bp: Initial: 30012263 bp After Masking: 22256535 bp Masked: 25.84 % -- Input Database Coverage: 40064478 bp out of 520636573 bp ( 7.70 % ) Sampling Time: 00:03:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 412686 Comparison Time: 00:15:15 (hh:mm:ss) Elapsed Time, 36513 HSPs Collected Number of families returned by RECON: 4294 Round Time: 00:19:28 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58939 repeats masked totaling 10048364 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90124008 bp Num Contigs Represented = 744 Non ambiguous bp: Initial: 90019639 bp After Masking: 66954135 bp Masked: 25.62 % -- Input Database Coverage: 130188486 bp out of 520636573 bp ( 25.01 % ) Sampling Time: 00:10:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3719628 Comparison Time: 01:32:19 (hh:mm:ss) Elapsed Time, 295254 HSPs Collected Number of families returned by RECON: 16060 Round Time: 01:47:14 (hh:mm:ss) Elapsed Time : 421 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 229454 repeats masked totaling 42954092 bp(s). - TE Masking time 00:03:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270349584 bp Num Contigs Represented = 1986 Non ambiguous bp: Initial: 270028565 bp After Masking: 187473334 bp Masked: 30.57 % -- Input Database Coverage: 400538070 bp out of 520636573 bp ( 76.93 % ) Sampling Time: 00:32:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32332861 Comparison Time: 10:37:13 (hh:mm:ss) Elapsed Time, 987489 HSPs Collected Number of families returned by RECON: 57264 Round Time: 11:46:10 (hh:mm:ss) Elapsed Time : 1036 families discovered. RepeatScout/RECON discovery complete: 2012 families found Classification Time: 00:51:45 (hh:mm:ss) Elapsed Time Program Time: 15:01:32 (hh:mm:ss) Elapsed Time