RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Cfv3vm/RM_19379.SunMay71319322023 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: 1683490770 Database = /dev/shm/rModeler.Cfv3vm/GCA_023637945.1_DD_ASM_B1 - Sequences = 70 - Bases = 1020112811 Storage Throughput = excellent ( 1165.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40177142 bp ( 40015344 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:06 (hh:mm:ss) Elapsed Time Round Time: 00:28:15 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2173 repeats masked totaling 608908 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10046033 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10005681 bp After Masking: 9291864 bp Masked: 7.13 % -- Input Database Coverage: 10046033 bp out of 1020112811 bp ( 0.98 % ) Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:11:51 (hh:mm:ss) Elapsed Time, 509 HSPs Collected Number of families returned by RECON: 269 Round Time: 00:13:49 (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 : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6391 repeats masked totaling 1766756 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30131096 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30009650 bp After Masking: 28039597 bp Masked: 6.56 % -- Input Database Coverage: 40177129 bp out of 1020112811 bp ( 3.94 % ) Sampling Time: 00:02:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:59:40 (hh:mm:ss) Elapsed Time, 3916 HSPs Collected Number of families returned by RECON: 1717 Round Time: 01:02:47 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19297 repeats masked totaling 5394268 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90435573 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90005979 bp After Masking: 83755365 bp Masked: 6.94 % -- Input Database Coverage: 130612702 bp out of 1020112811 bp ( 12.80 % ) Sampling Time: 00:08:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 06:25:33 (hh:mm:ss) Elapsed Time, 30503 HSPs Collected Number of families returned by RECON: 11889 Round Time: 06:39:21 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64709 repeats masked totaling 17811589 bp(s). - TE Masking time 00:02:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270909331 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 270007139 bp After Masking: 249945692 bp Masked: 7.43 % -- Input Database Coverage: 401522033 bp out of 1020112811 bp ( 39.36 % ) Sampling Time: 00:25:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 48:40:49 (hh:mm:ss) Elapsed Time, 187629 HSPs Collected Number of families returned by RECON: 80704 Round Time: 50:30:22 (hh:mm:ss) Elapsed Time : 151 families discovered. RepeatScout/RECON discovery complete: 274 families found Classification Time: 00:14:56 (hh:mm:ss) Elapsed Time Program Time: 59:09:30 (hh:mm:ss) Elapsed Time