RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.9RAZ9i/RM_1149090.TueNov121154162024 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: 1731441256 Database = /scratch/tmp/rModeler.9RAZ9i/GCA_964187855.1_kmMyxGlut1.1 - Sequences = 4004 - Bases = 3057523704 - N50 = 212066388 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 418641039-448543899 | [ 1 ] 388738179-418641038 | [ ] 358835319-388738178 | [ ] 328932459-358835318 | [ ] 299029599-328932458 | [ ] 269126739-299029598 | [ 1 ] 239223879-269126738 | [ ] 209321019-239223878 | [ 3 ] 179418159-209321018 | [ 2 ] 149515299-179418158 | [ 2 ] 119612439-149515298 | [ 2 ] 89709579-119612438 | [ 2 ] 59806719-89709578 | [ 1 ] 29903859-59806718 | [ ] 1000-29903859 |************************************************** [ 3990 ] Storage Throughput = excellent ( 1614.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035599 bp ( 40024323 non ambiguous ) - Num Contigs Represented = 158 - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:25 (hh:mm:ss) Elapsed Time Round Time: 00:25:10 (hh:mm:ss) Elapsed Time : 816 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13921 repeats masked totaling 5490668 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025314 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10021914 bp After Masking: 2176028 bp Masked: 78.29 % -- Input Database Coverage: 10025314 bp out of 3057523704 bp ( 0.33 % ) Sampling Time: 00:03:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 7327 HSPs Collected Number of families returned by RECON: 785 Round Time: 00:06:16 (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 : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42769 repeats masked totaling 16528518 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010284 bp Num Contigs Represented = 128 Non ambiguous bp: Initial: 30002408 bp After Masking: 6576043 bp Masked: 78.08 % -- Input Database Coverage: 40035598 bp out of 3057523704 bp ( 1.31 % ) Sampling Time: 00:09:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296835 Comparison Time: 00:10:07 (hh:mm:ss) Elapsed Time, 32351 HSPs Collected Number of families returned by RECON: 2614 Round Time: 00:20:00 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 133947 repeats masked totaling 49967330 bp(s). - TE Masking time 00:01:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90060099 bp Num Contigs Represented = 369 Non ambiguous bp: Initial: 90032983 bp After Masking: 18913246 bp Masked: 78.99 % -- Input Database Coverage: 130095697 bp out of 3057523704 bp ( 4.25 % ) Sampling Time: 00:28:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2699326 Comparison Time: 00:43:13 (hh:mm:ss) Elapsed Time, 180166 HSPs Collected Number of families returned by RECON: 6509 Round Time: 01:14:44 (hh:mm:ss) Elapsed Time : 349 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:10:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 436097 repeats masked totaling 159639571 bp(s). - TE Masking time 00:05:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270092926 bp Num Contigs Represented = 893 Non ambiguous bp: Initial: 270011365 bp After Masking: 46184231 bp Masked: 82.90 % -- Input Database Coverage: 400188623 bp out of 3057523704 bp ( 13.09 % ) Sampling Time: 01:29:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23891328 Comparison Time: 03:31:18 (hh:mm:ss) Elapsed Time, 527165 HSPs Collected Number of families returned by RECON: 14786 Round Time: 05:10:48 (hh:mm:ss) Elapsed Time : 895 families discovered. RepeatScout/RECON discovery complete: 2134 families found Classification Time: 00:55:31 (hh:mm:ss) Elapsed Time Program Time: 08:12:29 (hh:mm:ss) Elapsed Time