RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DsRR3Z/RM_30272.MonJan21108202023 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: 1672686499 Database = /dev/shm/rModeler.DsRR3Z/GCF_017639745.1_fMelBoe1.pri - Sequences = 93 - Bases = 865592457 Storage Throughput = excellent ( 1067.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40167602 bp ( 40029403 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:00 (hh:mm:ss) Elapsed Time Round Time: 00:31:52 (hh:mm:ss) Elapsed Time : 653 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9400 repeats masked totaling 1999021 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10122661 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10029462 bp After Masking: 7715008 bp Masked: 23.08 % -- Input Database Coverage: 10122661 bp out of 865592457 bp ( 1.17 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:32 (hh:mm:ss) Elapsed Time, 7901 HSPs Collected Number of families returned by RECON: 1492 Round Time: 00:08:22 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28390 repeats masked totaling 6027499 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30084868 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30039868 bp After Masking: 22602701 bp Masked: 24.76 % -- Input Database Coverage: 40207529 bp out of 865592457 bp ( 4.65 % ) Sampling Time: 00:04:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:36:03 (hh:mm:ss) Elapsed Time, 49923 HSPs Collected Number of families returned by RECON: 5177 Round Time: 00:42:56 (hh:mm:ss) Elapsed Time : 121 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 96899 repeats masked totaling 20665105 bp(s). - TE Masking time 00:02:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90488872 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 90014584 bp After Masking: 65679859 bp Masked: 27.03 % -- Input Database Coverage: 130696401 bp out of 865592457 bp ( 15.10 % ) Sampling Time: 00:11:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 04:14:19 (hh:mm:ss) Elapsed Time, 285610 HSPs Collected Number of families returned by RECON: 16453 Round Time: 04:41:39 (hh:mm:ss) Elapsed Time : 537 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 352305 repeats masked totaling 75675165 bp(s). - TE Masking time 00:15:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270830966 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 270003614 bp After Masking: 183621958 bp Masked: 31.99 % -- Input Database Coverage: 401527367 bp out of 865592457 bp ( 46.39 % ) Sampling Time: 00:42:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23014720 Comparison Time: 32:13:51 (hh:mm:ss) Elapsed Time, 738227 HSPs Collected Number of families returned by RECON: 56339 Round Time: 34:41:09 (hh:mm:ss) Elapsed Time : 1273 families discovered. RepeatScout/RECON discovery complete: 2597 families found Classification Time: 02:19:05 (hh:mm:ss) Elapsed Time Program Time: 43:05:03 (hh:mm:ss) Elapsed Time