RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Zx71q6/RM_28377.TueJul20213232024 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: 1719911603 Database = /dev/shm/rModeler.Zx71q6/GCA_037039145.1_fFunDia1.hap1 - Sequences = 331 - Bases = 1351828608 - N50 = 58007302 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 61506669-65899194 | [ 5 ] 57114144-61506668 |* [ 7 ] 52721620-57114144 | [ 5 ] 48329095-52721619 | [ 3 ] 43936570-48329094 | [ 3 ] 39544046-43936570 | [ ] 35151521-39544045 | [ ] 30758996-35151520 | [ 1 ] 26366472-30758996 | [ ] 21973947-26366471 | [ ] 17581422-21973946 | [ ] 13188898-17581422 | [ ] 8796373-13188897 | [ ] 4403848-8796372 | [ ] 11324-4403848 |************************************************** [ 307 ] Storage Throughput = excellent ( 1033.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40086188 bp ( 40013152 non ambiguous ) - Num Contigs Represented = 49 - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:13 (hh:mm:ss) Elapsed Time Round Time: 00:33:06 (hh:mm:ss) Elapsed Time : 863 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13785 repeats masked totaling 3646905 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023092 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10022892 bp After Masking: 5954645 bp Masked: 40.59 % -- Input Database Coverage: 10023092 bp out of 1351828608 bp ( 0.74 % ) Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:57 (hh:mm:ss) Elapsed Time, 9873 HSPs Collected Number of families returned by RECON: 1497 Round Time: 00:06:42 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44737 repeats masked totaling 11603782 bp(s). - TE Masking time 00:01:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30103095 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30030259 bp After Masking: 17242105 bp Masked: 42.58 % -- Input Database Coverage: 40126187 bp out of 1351828608 bp ( 2.97 % ) Sampling Time: 00:03:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:24:54 (hh:mm:ss) Elapsed Time, 64244 HSPs Collected Number of families returned by RECON: 4231 Round Time: 00:30:37 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 150341 repeats masked totaling 37587196 bp(s). - TE Masking time 00:03:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90311091 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 90034551 bp After Masking: 49223412 bp Masked: 45.33 % -- Input Database Coverage: 130437278 bp out of 1351828608 bp ( 9.65 % ) Sampling Time: 00:11:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 02:42:55 (hh:mm:ss) Elapsed Time, 270472 HSPs Collected Number of families returned by RECON: 11488 Round Time: 03:05:07 (hh:mm:ss) Elapsed Time : 522 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:44 (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... 518738 repeats masked totaling 128525408 bp(s). - TE Masking time 00:16:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270867060 bp Num Contigs Represented = 119 Non ambiguous bp: Initial: 270034710 bp After Masking: 132126432 bp Masked: 51.07 % -- Input Database Coverage: 401304338 bp out of 1351828608 bp ( 29.69 % ) Sampling Time: 00:40:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23109801 Comparison Time: 23:14:04 (hh:mm:ss) Elapsed Time, 843381 HSPs Collected Number of families returned by RECON: 33434 Round Time: 24:49:57 (hh:mm:ss) Elapsed Time : 1138 families discovered. RepeatScout/RECON discovery complete: 2703 families found Classification Time: 02:26:49 (hh:mm:ss) Elapsed Time Program Time: 31:32:18 (hh:mm:ss) Elapsed Time