RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4imLVc/RM_3023120.SatJul192224102025 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: 1752989050 Database = /dev/shm/rModeler.4imLVc/GCA_048593345.1_ASM4859334v1 - Sequences = 8 - Bases = 3250186738 Storage Throughput = excellent ( 1587.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000341 bp ( 40000341 non ambiguous ) - Num Contigs Represented = 8 - Sequence extraction : 00:04:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:34 (hh:mm:ss) Elapsed Time Round Time: 00:16:18 (hh:mm:ss) Elapsed Time : 325 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20900 repeats masked totaling 3885751 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 9999993 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 9999993 bp After Masking: 6011931 bp Masked: 39.88 % -- Input Database Coverage: 9999993 bp out of 3250186738 bp ( 0.31 % ) Sampling Time: 00:01:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:12 (hh:mm:ss) Elapsed Time, 15169 HSPs Collected Number of families returned by RECON: 1267 Round Time: 00:05:01 (hh:mm:ss) Elapsed Time : 40 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 69604 repeats masked totaling 13381080 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000268 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 30000268 bp After Masking: 16251586 bp Masked: 45.83 % -- Input Database Coverage: 40000261 bp out of 3250186738 bp ( 1.23 % ) Sampling Time: 00:04:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:12:36 (hh:mm:ss) Elapsed Time, 23021 HSPs Collected Number of families returned by RECON: 2941 Round Time: 00:17:52 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 228875 repeats masked totaling 42208513 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034222 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 90034222 bp After Masking: 46839820 bp Masked: 47.98 % -- Input Database Coverage: 130034483 bp out of 3250186738 bp ( 4.00 % ) Sampling Time: 00:13:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:05:40 (hh:mm:ss) Elapsed Time, 81487 HSPs Collected Number of families returned by RECON: 10264 Round Time: 01:20:53 (hh:mm:ss) Elapsed Time : 176 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:33:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 719850 repeats masked totaling 134017281 bp(s). - TE Masking time 00:02:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270024506 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 270024506 bp After Masking: 132888944 bp Masked: 50.79 % -- Input Database Coverage: 400058989 bp out of 3250186738 bp ( 12.31 % ) Sampling Time: 00:42:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22784625 Comparison Time: 07:16:35 (hh:mm:ss) Elapsed Time, 294891 HSPs Collected Number of families returned by RECON: 37506 Round Time: 08:11:48 (hh:mm:ss) Elapsed Time : 516 families discovered. RepeatScout/RECON discovery complete: 1116 families found Classification Time: 00:17:13 (hh:mm:ss) Elapsed Time Program Time: 10:29:05 (hh:mm:ss) Elapsed Time