RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.THrX5v/RM_21482.WedNov131905322024 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: 1731553532 Database = /scratch/tmp/rModeler.THrX5v/GCA_035047305.1_BraPum1.0 - Sequences = 21 - Bases = 2486266449 Storage Throughput = fair ( 588.37 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000905 bp ( 40000905 non ambiguous ) - Num Contigs Represented = 18 - Sequence extraction : 00:06:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:14 (hh:mm:ss) Elapsed Time Round Time: 00:40:47 (hh:mm:ss) Elapsed Time : 649 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16474 repeats masked totaling 5252173 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000184 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 10000184 bp After Masking: 4204916 bp Masked: 57.95 % -- Input Database Coverage: 10000184 bp out of 2486266449 bp ( 0.40 % ) Sampling Time: 00:06:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:43 (hh:mm:ss) Elapsed Time, 5531 HSPs Collected Number of families returned by RECON: 946 Round Time: 00:11:26 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:05:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49740 repeats masked totaling 16291278 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000641 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 30000641 bp After Masking: 12589764 bp Masked: 58.04 % -- Input Database Coverage: 40000825 bp out of 2486266449 bp ( 1.61 % ) Sampling Time: 00:15:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:21:33 (hh:mm:ss) Elapsed Time, 30936 HSPs Collected Number of families returned by RECON: 3003 Round Time: 00:37:53 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:15:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 161638 repeats masked totaling 49326500 bp(s). - TE Masking time 00:02:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031798 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 90031698 bp After Masking: 36692945 bp Masked: 59.24 % -- Input Database Coverage: 130032623 bp out of 2486266449 bp ( 5.23 % ) Sampling Time: 00:50:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:06:46 (hh:mm:ss) Elapsed Time, 171130 HSPs Collected Number of families returned by RECON: 8677 Round Time: 03:05:37 (hh:mm:ss) Elapsed Time : 350 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:47:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:53:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 531244 repeats masked totaling 157772704 bp(s). - TE Masking time 00:10:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270007044 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 270007044 bp After Masking: 98982065 bp Masked: 63.34 % -- Input Database Coverage: 400039667 bp out of 2486266449 bp ( 16.09 % ) Sampling Time: 02:52:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 14:27:41 (hh:mm:ss) Elapsed Time, 461501 HSPs Collected Number of families returned by RECON: 24224 Round Time: 17:58:42 (hh:mm:ss) Elapsed Time : 817 families discovered. RepeatScout/RECON discovery complete: 1906 families found Classification Time: 01:15:32 (hh:mm:ss) Elapsed Time Program Time: 23:49:57 (hh:mm:ss) Elapsed Time