RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2h49NJ/RM_105235.SatJan141057452023 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: 1673722663 Database = /dev/shm/rModeler.2h49NJ/GCF_009819535.1_rLacAgi1.pri - Sequences = 29 - Bases = 1391404169 Storage Throughput = good ( 990.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40103994 bp ( 40011788 non ambiguous ) - Num Contigs Represented = 20 - Sequence extraction : 00:02:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:16 (hh:mm:ss) Elapsed Time Round Time: 00:24:04 (hh:mm:ss) Elapsed Time : 578 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18494 repeats masked totaling 3032423 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022548 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10021822 bp After Masking: 6844115 bp Masked: 31.71 % -- Input Database Coverage: 10022548 bp out of 1391404169 bp ( 0.72 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:54 (hh:mm:ss) Elapsed Time, 8856 HSPs Collected Number of families returned by RECON: 1321 Round Time: 00:07:25 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57851 repeats masked totaling 9341044 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30121525 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 30030045 bp After Masking: 20348482 bp Masked: 32.24 % -- Input Database Coverage: 40144073 bp out of 1391404169 bp ( 2.89 % ) Sampling Time: 00:03:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:29:07 (hh:mm:ss) Elapsed Time, 48376 HSPs Collected Number of families returned by RECON: 4819 Round Time: 00:34:07 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 185903 repeats masked totaling 29941992 bp(s). - TE Masking time 00:01:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90244730 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 90012621 bp After Masking: 59120869 bp Masked: 34.32 % -- Input Database Coverage: 130388803 bp out of 1391404169 bp ( 9.37 % ) Sampling Time: 00:09:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 02:56:09 (hh:mm:ss) Elapsed Time, 205247 HSPs Collected Number of families returned by RECON: 15378 Round Time: 03:17:49 (hh:mm:ss) Elapsed Time : 469 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 631784 repeats masked totaling 101400384 bp(s). - TE Masking time 00:08:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270565754 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 270019099 bp After Masking: 165864900 bp Masked: 38.57 % -- Input Database Coverage: 400954557 bp out of 1391404169 bp ( 28.82 % ) Sampling Time: 00:31:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22885995 Comparison Time: 19:01:53 (hh:mm:ss) Elapsed Time, 532343 HSPs Collected Number of families returned by RECON: 54397 Round Time: 20:59:50 (hh:mm:ss) Elapsed Time : 1106 families discovered. RepeatScout/RECON discovery complete: 2309 families found Classification Time: 01:13:07 (hh:mm:ss) Elapsed Time Program Time: 26:36:22 (hh:mm:ss) Elapsed Time