RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.aUv7xc/RM_1525001.SatJul130609362024 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: 1720876175 Database = /dev/shm/rModeler.aUv7xc/GCF_027580225.1_HAU_Mang_1.0 - Sequences = 358 - Bases = 1104586043 - N50 = 43291699 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 62539521-67006559 | [ 1 ] 58072484-62539521 | [ 1 ] 53605447-58072484 | [ 1 ] 49138409-53605446 | [ 3 ] 44671372-49138409 | [ 2 ] 40204335-44671372 |* [ 7 ] 35737298-40204335 | [ 6 ] 31270260-35737297 | [ 4 ] 26803223-31270260 | [ ] 22336186-26803223 | [ ] 17869149-22336186 | [ ] 13402111-17869148 | [ ] 8935074-13402111 | [ ] 4468037-8935074 | [ ] 1000-4468037 |************************************************** [ 333 ] Storage Throughput = excellent ( 1509.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013330 bp ( 40011412 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:05 (hh:mm:ss) Elapsed Time Round Time: 00:24:22 (hh:mm:ss) Elapsed Time : 1332 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21640 repeats masked totaling 4563657 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015883 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10015183 bp After Masking: 5148704 bp Masked: 48.59 % -- Input Database Coverage: 10015883 bp out of 1104586043 bp ( 0.91 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:41 (hh:mm:ss) Elapsed Time, 5188 HSPs Collected Number of families returned by RECON: 1256 Round Time: 00:07:11 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64119 repeats masked totaling 13920627 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037448 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30036230 bp After Masking: 15194610 bp Masked: 49.41 % -- Input Database Coverage: 40053331 bp out of 1104586043 bp ( 3.63 % ) Sampling Time: 00:04:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:26:19 (hh:mm:ss) Elapsed Time, 39729 HSPs Collected Number of families returned by RECON: 3940 Round Time: 00:31:54 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 198747 repeats masked totaling 41793061 bp(s). - TE Masking time 00:03:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030041 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90024159 bp After Masking: 45171183 bp Masked: 49.82 % -- Input Database Coverage: 130083372 bp out of 1104586043 bp ( 11.78 % ) Sampling Time: 00:19:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 03:02:33 (hh:mm:ss) Elapsed Time, 339322 HSPs Collected Number of families returned by RECON: 11592 Round Time: 03:33:46 (hh:mm:ss) Elapsed Time : 620 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 656812 repeats masked totaling 142999163 bp(s). - TE Masking time 00:16:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019828 bp Num Contigs Represented = 137 Non ambiguous bp: Initial: 270004628 bp After Masking: 118518632 bp Masked: 56.10 % -- Input Database Coverage: 400103200 bp out of 1104586043 bp ( 36.22 % ) Sampling Time: 00:45:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23211891 Comparison Time: 14:59:15 (hh:mm:ss) Elapsed Time, 1001204 HSPs Collected Number of families returned by RECON: 32382 Round Time: 16:29:56 (hh:mm:ss) Elapsed Time : 1435 families discovered. RepeatScout/RECON discovery complete: 3476 families found Classification Time: 02:22:52 (hh:mm:ss) Elapsed Time Program Time: 23:30:01 (hh:mm:ss) Elapsed Time