RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BLxt8k/RM_720.ThuDec71617252023 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: 1701994643 Database = /dev/shm/rModeler.BLxt8k/GCA_949987555.1_fBorAnt1.1 - Sequences = 1378 - Bases = 909249001 - N50 = 27475133 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 57594119-61707914 | [ 1 ] 53480325-57594119 | [ ] 49366531-53480325 | [ ] 45252736-49366530 | [ ] 41138942-45252736 | [ 1 ] 37025148-41138942 | [ 1 ] 32911354-37025148 | [ 2 ] 28797559-32911353 | [ 5 ] 24683765-28797559 | [ 7 ] 20569971-24683765 | [ 5 ] 16456177-20569971 | [ 2 ] 12342382-16456176 | [ 1 ] 8228588-12342382 | [ 1 ] 4114794-8228588 | [ 9 ] 1000-4114794 |************************************************** [ 1343 ] Storage Throughput = good ( 765.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40044064 bp ( 40020392 non ambiguous ) - Num Contigs Represented = 166 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:24 (hh:mm:ss) Elapsed Time Round Time: 00:42:38 (hh:mm:ss) Elapsed Time : 797 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9986 repeats masked totaling 2234355 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039507 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 10032472 bp After Masking: 5349812 bp Masked: 46.68 % -- Input Database Coverage: 10039507 bp out of 909249001 bp ( 1.10 % ) Sampling Time: 00:04:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:05:48 (hh:mm:ss) Elapsed Time, 49461 HSPs Collected Number of families returned by RECON: 1278 Round Time: 00:10:52 (hh:mm:ss) Elapsed Time : 10 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 00:10:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31933 repeats masked totaling 6996176 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30044527 bp Num Contigs Represented = 134 Non ambiguous bp: Initial: 30027890 bp After Masking: 16065310 bp Masked: 46.50 % -- Input Database Coverage: 40084034 bp out of 909249001 bp ( 4.41 % ) Sampling Time: 00:12:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 303810 Comparison Time: 00:26:30 (hh:mm:ss) Elapsed Time, 44908 HSPs Collected Number of families returned by RECON: 4585 Round Time: 00:40:20 (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 : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 102151 repeats masked totaling 22251814 bp(s). - TE Masking time 00:02:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90052613 bp Num Contigs Represented = 280 Non ambiguous bp: Initial: 90005013 bp After Masking: 48145031 bp Masked: 46.51 % -- Input Database Coverage: 130136647 bp out of 909249001 bp ( 14.31 % ) Sampling Time: 00:36:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2713285 Comparison Time: 02:43:36 (hh:mm:ss) Elapsed Time, 363977 HSPs Collected Number of families returned by RECON: 13971 Round Time: 03:41:01 (hh:mm:ss) Elapsed Time : 602 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:34:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 369345 repeats masked totaling 82391510 bp(s). - TE Masking time 00:15:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270176731 bp Num Contigs Represented = 573 Non ambiguous bp: Initial: 270017333 bp After Masking: 129513711 bp Masked: 52.04 % -- Input Database Coverage: 400313378 bp out of 909249001 bp ( 44.03 % ) Sampling Time: 01:53:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24363690 Comparison Time: 19:31:23 (hh:mm:ss) Elapsed Time, 1028450 HSPs Collected Number of families returned by RECON: 44716 Round Time: 22:52:20 (hh:mm:ss) Elapsed Time : 1359 families discovered. RepeatScout/RECON discovery complete: 2848 families found Classification Time: 02:28:08 (hh:mm:ss) Elapsed Time Program Time: 30:35:19 (hh:mm:ss) Elapsed Time