RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5SxslK/RM_1939576.FriJan310912522025 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: 1738343571 Database = /dev/shm/rModeler.5SxslK/GCA_030295235.1_Fsolaris_ONT_v03 - Sequences = 62 - Bases = 51725046 Storage Throughput = excellent ( 1624.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017071 bp ( 40017071 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:56 (hh:mm:ss) Elapsed Time Round Time: 00:08:08 (hh:mm:ss) Elapsed Time : 118 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2316 repeats masked totaling 488843 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007825 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10007825 bp After Masking: 9418454 bp Masked: 5.89 % -- Input Database Coverage: 10007825 bp out of 51725046 bp ( 19.35 % ) Sampling Time: 00:00:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:02:40 (hh:mm:ss) Elapsed Time, 3843 HSPs Collected Number of families returned by RECON: 866 Round Time: 00:02:55 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6689 repeats masked totaling 1446287 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009178 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30009178 bp After Masking: 28215133 bp Masked: 5.98 % -- Input Database Coverage: 40017003 bp out of 51725046 bp ( 77.36 % ) Sampling Time: 00:00:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296835 Comparison Time: 00:12:18 (hh:mm:ss) Elapsed Time, 29538 HSPs Collected Number of families returned by RECON: 3926 Round Time: 00:13:02 (hh:mm:ss) Elapsed Time : 4 families discovered. - Increasing sample size to include end piece now = 101717221 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 101717221 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2793 repeats masked totaling 550071 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11707786 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 11707786 bp After Masking: 10981783 bp Masked: 6.20 % -- Input Database Coverage: 51724789 bp out of 51725046 bp ( 100.00 % ) Sampling Time: 00:00:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 44253 Comparison Time: 00:03:15 (hh:mm:ss) Elapsed Time, 3516 HSPs Collected Number of families returned by RECON: 1037 Round Time: 00:03:29 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 123 families found Classification Time: 00:02:50 (hh:mm:ss) Elapsed Time Program Time: 00:30:24 (hh:mm:ss) Elapsed Time