RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/refseqBuild/GCF/900/324/465/GCF_900324465.2_fAnaTes1.2/trackData/repeatModeler/RM_25516.WedDec282145582022 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: 1672292756 Database = /hive/data/genomes/asmHubs/refseqBuild/GCF/900/324/465/GCF_900324465.2_fAnaTes1.2/trackData/repeatModeler/GCF_900324465.2_fAnaTes1.2 - Sequences = 51 - Bases = 555658001 Storage Throughput = good ( 758.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40167874 bp ( 40001931 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:57 (hh:mm:ss) Elapsed Time Round Time: 00:24:29 (hh:mm:ss) Elapsed Time : 189 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 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3431 repeats masked totaling 704843 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10042072 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10035179 bp After Masking: 9184942 bp Masked: 8.47 % -- Input Database Coverage: 10042072 bp out of 555658001 bp ( 1.81 % ) Sampling Time: 00:00:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:38 (hh:mm:ss) Elapsed Time, 4504 HSPs Collected Number of families returned by RECON: 1078 Round Time: 00:08:09 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10625 repeats masked totaling 2085908 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30165727 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30006677 bp After Masking: 27523145 bp Masked: 8.28 % -- Input Database Coverage: 40207799 bp out of 555658001 bp ( 7.24 % ) Sampling Time: 00:02:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:38:10 (hh:mm:ss) Elapsed Time, 30969 HSPs Collected Number of families returned by RECON: 4522 Round Time: 00:45:22 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38218 repeats masked totaling 7276404 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90612458 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90019327 bp After Masking: 81470044 bp Masked: 9.50 % -- Input Database Coverage: 130820257 bp out of 555658001 bp ( 23.54 % ) Sampling Time: 00:06:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 04:42:38 (hh:mm:ss) Elapsed Time, 189422 HSPs Collected Number of families returned by RECON: 19760 Round Time: 05:29:34 (hh:mm:ss) Elapsed Time : 287 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 00:11:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 159655 repeats masked totaling 29518958 bp(s). - TE Masking time 00:06:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271766029 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 270019274 bp After Masking: 236641561 bp Masked: 12.36 % -- Input Database Coverage: 402586286 bp out of 555658001 bp ( 72.45 % ) Sampling Time: 00:22:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23177836 Comparison Time: 37:21:42 (hh:mm:ss) Elapsed Time, 654932 HSPs Collected Number of families returned by RECON: 84441 Round Time: 43:07:05 (hh:mm:ss) Elapsed Time : 775 families discovered. RepeatScout/RECON discovery complete: 1314 families found Classification Time: 01:19:44 (hh:mm:ss) Elapsed Time Program Time: 51:14:23 (hh:mm:ss) Elapsed Time