RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.l4GGgj/RM_64348.FriApr250716262025 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: 1745590586 Database = /dev/shm/rModeler.l4GGgj/GCA_048301585.1_ASM4830158v1 - Sequences = 70 - Bases = 953377980 Storage Throughput = excellent ( 1895.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033267 bp ( 40033267 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:13 (hh:mm:ss) Elapsed Time Round Time: 00:18:01 (hh:mm:ss) Elapsed Time : 1156 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18406 repeats masked totaling 3153357 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001408 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10001408 bp After Masking: 5772569 bp Masked: 42.28 % -- Input Database Coverage: 10001408 bp out of 953377980 bp ( 1.05 % ) Sampling Time: 00:01:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:42 (hh:mm:ss) Elapsed Time, 9287 HSPs Collected Number of families returned by RECON: 1704 Round Time: 00:04:52 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57126 repeats masked totaling 9560230 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031838 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30031838 bp After Masking: 17688947 bp Masked: 41.10 % -- Input Database Coverage: 40033246 bp out of 953377980 bp ( 4.20 % ) Sampling Time: 00:05:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:12:06 (hh:mm:ss) Elapsed Time, 82729 HSPs Collected Number of families returned by RECON: 5655 Round Time: 00:18:38 (hh:mm:ss) Elapsed Time : 210 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 192079 repeats masked totaling 31719370 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010405 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90010405 bp After Masking: 50540528 bp Masked: 43.85 % -- Input Database Coverage: 130043651 bp out of 953377980 bp ( 13.64 % ) Sampling Time: 00:17:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:09:22 (hh:mm:ss) Elapsed Time, 663351 HSPs Collected Number of families returned by RECON: 14680 Round Time: 01:32:23 (hh:mm:ss) Elapsed Time : 699 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:43:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 653276 repeats masked totaling 113978274 bp(s). - TE Masking time 00:04:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034989 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 270034989 bp After Masking: 132394823 bp Masked: 50.97 % -- Input Database Coverage: 400078640 bp out of 953377980 bp ( 41.96 % ) Sampling Time: 00:50:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 07:28:28 (hh:mm:ss) Elapsed Time, 1701570 HSPs Collected Number of families returned by RECON: 42088 Round Time: 08:43:36 (hh:mm:ss) Elapsed Time : 1353 families discovered. RepeatScout/RECON discovery complete: 3437 families found Classification Time: 00:49:49 (hh:mm:ss) Elapsed Time Program Time: 11:47:19 (hh:mm:ss) Elapsed Time