RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.IvLqNU/RM_2810433.FriJan121056372024 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: 1705085797 Database = /dev/shm/rModeler.IvLqNU/GCA_918807975.1_kaAplTurb1.1 - Sequences = 27 - Bases = 605507883 Storage Throughput = excellent ( 1156.18 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005128 bp ( 40002728 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:34 (hh:mm:ss) Elapsed Time Round Time: 00:26:30 (hh:mm:ss) Elapsed Time : 1216 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18660 repeats masked totaling 4640552 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10017711 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10017711 bp After Masking: 4996729 bp Masked: 50.12 % -- Input Database Coverage: 10017711 bp out of 605507883 bp ( 1.65 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:13 (hh:mm:ss) Elapsed Time, 7810 HSPs Collected Number of families returned by RECON: 1328 Round Time: 00:06:54 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56562 repeats masked totaling 14173278 bp(s). - TE Masking time 00:01:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027348 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 30024948 bp After Masking: 14641426 bp Masked: 51.24 % -- Input Database Coverage: 40045059 bp out of 605507883 bp ( 6.61 % ) Sampling Time: 00:04:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:29:35 (hh:mm:ss) Elapsed Time, 52508 HSPs Collected Number of families returned by RECON: 3929 Round Time: 00:35:44 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 176081 repeats masked totaling 42447057 bp(s). - TE Masking time 00:05:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013349 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 90010549 bp After Masking: 43173678 bp Masked: 52.03 % -- Input Database Coverage: 130058408 bp out of 605507883 bp ( 21.48 % ) Sampling Time: 00:13:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 04:48:58 (hh:mm:ss) Elapsed Time, 364970 HSPs Collected Number of families returned by RECON: 10565 Round Time: 05:15:42 (hh:mm:ss) Elapsed Time : 672 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 603314 repeats masked totaling 148397271 bp(s). - TE Masking time 00:22:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270045178 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 270037178 bp After Masking: 110183780 bp Masked: 59.20 % -- Input Database Coverage: 400103586 bp out of 605507883 bp ( 66.08 % ) Sampling Time: 00:45:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 17:03:56 (hh:mm:ss) Elapsed Time, 875280 HSPs Collected Number of families returned by RECON: 29339 Round Time: 18:58:23 (hh:mm:ss) Elapsed Time : 1428 families discovered. RepeatScout/RECON discovery complete: 3402 families found Classification Time: 03:06:51 (hh:mm:ss) Elapsed Time Program Time: 28:30:04 (hh:mm:ss) Elapsed Time