RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3HJJfS/RM_12846.SunJan150359212023 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: 1673783960 Database = /dev/shm/rModeler.3HJJfS/GCA_024294585.1_rVipLat1.pri - Sequences = 56 - Bases = 1631568913 Storage Throughput = excellent ( 1059.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40043437 bp ( 40030885 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:04:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:15 (hh:mm:ss) Elapsed Time Round Time: 00:31:03 (hh:mm:ss) Elapsed Time : 517 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14581 repeats masked totaling 3861272 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040349 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 10032156 bp After Masking: 5776252 bp Masked: 42.42 % -- Input Database Coverage: 10040349 bp out of 1631568913 bp ( 0.62 % ) Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:18 (hh:mm:ss) Elapsed Time, 4664 HSPs Collected Number of families returned by RECON: 824 Round Time: 00:08:43 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44846 repeats masked totaling 11930013 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30043008 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30038649 bp After Masking: 16876224 bp Masked: 43.82 % -- Input Database Coverage: 40083357 bp out of 1631568913 bp ( 2.46 % ) Sampling Time: 00:05:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:29:23 (hh:mm:ss) Elapsed Time, 28315 HSPs Collected Number of families returned by RECON: 2843 Round Time: 00:36:23 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140626 repeats masked totaling 37127128 bp(s). - TE Masking time 00:02:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90141294 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90008537 bp After Masking: 49153396 bp Masked: 45.39 % -- Input Database Coverage: 130224651 bp out of 1631568913 bp ( 7.98 % ) Sampling Time: 00:17:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 03:01:28 (hh:mm:ss) Elapsed Time, 121514 HSPs Collected Number of families returned by RECON: 8570 Round Time: 03:26:03 (hh:mm:ss) Elapsed Time : 274 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:29:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 465736 repeats masked totaling 118646582 bp(s). - TE Masking time 00:09:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270617271 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 270030980 bp After Masking: 140386489 bp Masked: 48.01 % -- Input Database Coverage: 400841922 bp out of 1631568913 bp ( 24.57 % ) Sampling Time: 00:58:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 22:25:01 (hh:mm:ss) Elapsed Time, 455964 HSPs Collected Number of families returned by RECON: 31776 Round Time: 24:03:22 (hh:mm:ss) Elapsed Time : 773 families discovered. RepeatScout/RECON discovery complete: 1643 families found Classification Time: 01:11:16 (hh:mm:ss) Elapsed Time Program Time: 29:56:50 (hh:mm:ss) Elapsed Time