RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.TZizDL/RM_1377970.FriJul181029532025 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: 1752859793 Database = /dev/shm/rModeler.TZizDL/GCA_047715955.1_rBraPum1.hap2 - Sequences = 82 - Bases = 2479053460 Storage Throughput = excellent ( 1681.44 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003505 bp ( 40003505 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:03:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:10 (hh:mm:ss) Elapsed Time Round Time: 00:17:01 (hh:mm:ss) Elapsed Time : 682 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17206 repeats masked totaling 5205653 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000586 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10000586 bp After Masking: 4410448 bp Masked: 55.90 % -- Input Database Coverage: 10000586 bp out of 2479053460 bp ( 0.40 % ) Sampling Time: 00:02:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:39 (hh:mm:ss) Elapsed Time, 4506 HSPs Collected Number of families returned by RECON: 895 Round Time: 00:05:39 (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 : 00:02:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50697 repeats masked totaling 15773284 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002839 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30002839 bp After Masking: 12444345 bp Masked: 58.52 % -- Input Database Coverage: 40003425 bp out of 2479053460 bp ( 1.61 % ) Sampling Time: 00:13:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:09:48 (hh:mm:ss) Elapsed Time, 30001 HSPs Collected Number of families returned by RECON: 2976 Round Time: 00:23:24 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 164816 repeats masked totaling 49698080 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026195 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90025595 bp After Masking: 36117869 bp Masked: 59.88 % -- Input Database Coverage: 130029620 bp out of 2479053460 bp ( 5.25 % ) Sampling Time: 00:29:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 00:50:24 (hh:mm:ss) Elapsed Time, 154635 HSPs Collected Number of families returned by RECON: 8328 Round Time: 01:21:42 (hh:mm:ss) Elapsed Time : 339 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:25:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:07:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 539384 repeats masked totaling 157669638 bp(s). - TE Masking time 00:03:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014305 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 270011705 bp After Masking: 98857205 bp Masked: 63.39 % -- Input Database Coverage: 400043925 bp out of 2479053460 bp ( 16.14 % ) Sampling Time: 01:36:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 05:16:45 (hh:mm:ss) Elapsed Time, 431472 HSPs Collected Number of families returned by RECON: 24343 Round Time: 07:04:13 (hh:mm:ss) Elapsed Time : 861 families discovered. RepeatScout/RECON discovery complete: 1973 families found Classification Time: 00:35:07 (hh:mm:ss) Elapsed Time Program Time: 09:47:06 (hh:mm:ss) Elapsed Time