RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.cTWfiH/RM_676423.MonJul210354352025 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: 1753095275 Database = /dev/shm/rModeler.cTWfiH/GCA_965231245.1_bZosLat1.hap2.1 - Sequences = 818 - Bases = 1047426550 - N50 = 74641368 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 144180253-154478772 | [ 1 ] 133881735-144180253 | [ ] 123583217-133881735 | [ ] 113284699-123583217 | [ 2 ] 102986181-113284699 | [ ] 92687663-102986181 | [ ] 82389145-92687663 | [ ] 72090626-82389144 | [ 2 ] 61792108-72090626 | [ ] 51493590-61792108 | [ 1 ] 41195072-51493590 | [ ] 30896554-41195072 | [ 3 ] 20598036-30896554 | [ 4 ] 10299518-20598036 | [ 7 ] 1000-10299518 |************************************************** [ 798 ] Storage Throughput = excellent ( 1822.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019452 bp ( 40013852 non ambiguous ) - Num Contigs Represented = 104 - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:08 (hh:mm:ss) Elapsed Time Round Time: 00:10:24 (hh:mm:ss) Elapsed Time : 162 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2675 repeats masked totaling 750623 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004977 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10003977 bp After Masking: 8855825 bp Masked: 11.48 % -- Input Database Coverage: 10004977 bp out of 1047426550 bp ( 0.96 % ) Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:19 (hh:mm:ss) Elapsed Time, 706 HSPs Collected Number of families returned by RECON: 334 Round Time: 00:03:59 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8170 repeats masked totaling 2203464 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014395 bp Num Contigs Represented = 87 Non ambiguous bp: Initial: 30009795 bp After Masking: 26303001 bp Masked: 12.35 % -- Input Database Coverage: 40019372 bp out of 1047426550 bp ( 3.82 % ) Sampling Time: 00:16:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:15:52 (hh:mm:ss) Elapsed Time, 23732 HSPs Collected Number of families returned by RECON: 1997 Round Time: 00:32:39 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26025 repeats masked totaling 7201033 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035999 bp Num Contigs Represented = 165 Non ambiguous bp: Initial: 90025009 bp After Masking: 79005829 bp Masked: 12.24 % -- Input Database Coverage: 130055371 bp out of 1047426550 bp ( 12.42 % ) Sampling Time: 00:05:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2618616 Comparison Time: 01:46:10 (hh:mm:ss) Elapsed Time, 245028 HSPs Collected Number of families returned by RECON: 12010 Round Time: 01:54:13 (hh:mm:ss) Elapsed Time : 101 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 85990 repeats masked totaling 26445112 bp(s). - TE Masking time 00:02:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270051067 bp Num Contigs Represented = 348 Non ambiguous bp: Initial: 270018993 bp After Masking: 231762321 bp Masked: 14.17 % -- Input Database Coverage: 400106438 bp out of 1047426550 bp ( 38.20 % ) Sampling Time: 00:17:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23560680 Comparison Time: 13:28:06 (hh:mm:ss) Elapsed Time, 3223759 HSPs Collected Number of families returned by RECON: 75085 Round Time: 14:20:16 (hh:mm:ss) Elapsed Time : 284 families discovered. RepeatScout/RECON discovery complete: 559 families found Classification Time: 00:22:48 (hh:mm:ss) Elapsed Time Program Time: 17:24:19 (hh:mm:ss) Elapsed Time