RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WLN6gD/RM_26624.FriJan121040182024 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: 1705084817 Database = /dev/shm/rModeler.WLN6gD/GCA_031876335.1_mHipLar1.pri - Sequences = 69 - Bases = 2338923724 Storage Throughput = excellent ( 1098.07 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001592 bp ( 40001373 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:03:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:10 (hh:mm:ss) Elapsed Time Round Time: 00:36:48 (hh:mm:ss) Elapsed Time : 204 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8025 repeats masked totaling 2163291 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000185 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 9999966 bp After Masking: 7512531 bp Masked: 24.87 % -- Input Database Coverage: 10000185 bp out of 2338923724 bp ( 0.43 % ) Sampling Time: 00:01:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:44 (hh:mm:ss) Elapsed Time, 13072 HSPs Collected Number of families returned by RECON: 909 Round Time: 00:09:31 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27695 repeats masked totaling 7758929 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001327 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30001327 bp After Masking: 21114286 bp Masked: 29.62 % -- Input Database Coverage: 40001512 bp out of 2338923724 bp ( 1.71 % ) Sampling Time: 00:09:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 01:10:50 (hh:mm:ss) Elapsed Time, 92587 HSPs Collected Number of families returned by RECON: 2260 Round Time: 01:23:40 (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 : 00:07:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 91700 repeats masked totaling 25748593 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90002037 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90001637 bp After Masking: 60509663 bp Masked: 32.77 % -- Input Database Coverage: 130003549 bp out of 2338923724 bp ( 5.56 % ) Sampling Time: 00:26:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 06:09:04 (hh:mm:ss) Elapsed Time, 353235 HSPs Collected Number of families returned by RECON: 8463 Round Time: 06:40:24 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:53:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 313996 repeats masked totaling 84821531 bp(s). - TE Masking time 00:06:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270033908 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 270031208 bp After Masking: 175501137 bp Masked: 35.01 % -- Input Database Coverage: 400037457 bp out of 2338923724 bp ( 17.10 % ) Sampling Time: 01:22:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 31:43:04 (hh:mm:ss) Elapsed Time, 4674332 HSPs Collected Number of families returned by RECON: 36475 Round Time: 33:42:27 (hh:mm:ss) Elapsed Time : 390 families discovered. RepeatScout/RECON discovery complete: 851 families found Classification Time: 00:42:52 (hh:mm:ss) Elapsed Time Program Time: 43:15:42 (hh:mm:ss) Elapsed Time