RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/genbankBuild/GCA/014/108/255/GCA_014108255.1_mRhiFer1.p/trackData/repeatModeler/RM_288562.ThuMay41503102023 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: 1683237788 Database = /hive/data/genomes/asmHubs/genbankBuild/GCA/014/108/255/GCA_014108255.1_mRhiFer1.p/trackData/repeatModeler/GCA_014108255.1_mRhiFer1.p - Sequences = 50 - Bases = 2072561339 Storage Throughput = good ( 751.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40275351 bp ( 40035307 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:52 (hh:mm:ss) Elapsed Time Round Time: 00:17:10 (hh:mm:ss) Elapsed Time : 188 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7249 repeats masked totaling 1862111 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10079783 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10039783 bp After Masking: 8103740 bp Masked: 19.28 % -- Input Database Coverage: 10079783 bp out of 2072561339 bp ( 0.49 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:09 (hh:mm:ss) Elapsed Time, 6254 HSPs Collected Number of families returned by RECON: 1049 Round Time: 00:09:14 (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 : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26552 repeats masked totaling 6733332 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30235488 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30035444 bp After Masking: 23068602 bp Masked: 23.20 % -- Input Database Coverage: 40315271 bp out of 2072561339 bp ( 1.95 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:26:43 (hh:mm:ss) Elapsed Time, 27287 HSPs Collected Number of families returned by RECON: 3031 Round Time: 00:32:30 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 93098 repeats masked totaling 23404515 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90878129 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 90018629 bp After Masking: 65962961 bp Masked: 26.72 % -- Input Database Coverage: 131193400 bp out of 2072561339 bp ( 6.33 % ) Sampling Time: 00:05:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 02:14:07 (hh:mm:ss) Elapsed Time, 79872 HSPs Collected Number of families returned by RECON: 10078 Round Time: 02:32:08 (hh:mm:ss) Elapsed Time : 173 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 322730 repeats masked totaling 77291801 bp(s). - TE Masking time 00:02:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272295470 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 270022949 bp After Masking: 190809336 bp Masked: 29.34 % -- Input Database Coverage: 403488870 bp out of 2072561339 bp ( 19.47 % ) Sampling Time: 00:17:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23171028 Comparison Time: 14:23:45 (hh:mm:ss) Elapsed Time, 209243 HSPs Collected Number of families returned by RECON: 40529 Round Time: 15:33:38 (hh:mm:ss) Elapsed Time : 320 families discovered. RepeatScout/RECON discovery complete: 775 families found Classification Time: 00:19:25 (hh:mm:ss) Elapsed Time Program Time: 19:24:05 (hh:mm:ss) Elapsed Time