RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kyWe6F/RM_113282.FriJan131736082023 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: 1673660167 Database = /dev/shm/rModeler.kyWe6F/GCF_014108415.1_mMolMol1.p - Sequences = 60 - Bases = 2315568481 Storage Throughput = excellent ( 1393.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40843952 bp ( 40006992 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:02:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:05 (hh:mm:ss) Elapsed Time Round Time: 00:25:08 (hh:mm:ss) Elapsed Time : 186 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 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11558 repeats masked totaling 3009683 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10121168 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10023315 bp After Masking: 6894980 bp Masked: 31.21 % -- Input Database Coverage: 10121168 bp out of 2315568481 bp ( 0.44 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:54 (hh:mm:ss) Elapsed Time, 6308 HSPs Collected Number of families returned by RECON: 923 Round Time: 00:07:25 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36682 repeats masked totaling 8762460 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30762812 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30023705 bp After Masking: 20885646 bp Masked: 30.44 % -- Input Database Coverage: 40883980 bp out of 2315568481 bp ( 1.77 % ) Sampling Time: 00:04:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296065 Comparison Time: 00:27:33 (hh:mm:ss) Elapsed Time, 23477 HSPs Collected Number of families returned by RECON: 2240 Round Time: 00:32:41 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121811 repeats masked totaling 30439578 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92098086 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 90031900 bp After Masking: 58626048 bp Masked: 34.88 % -- Input Database Coverage: 132982066 bp out of 2315568481 bp ( 5.74 % ) Sampling Time: 00:10:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2653056 Comparison Time: 02:55:36 (hh:mm:ss) Elapsed Time, 84494 HSPs Collected Number of families returned by RECON: 8260 Round Time: 03:10:34 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 394711 repeats masked totaling 97990799 bp(s). - TE Masking time 00:04:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 276223451 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 270006938 bp After Masking: 168785924 bp Masked: 37.49 % -- Input Database Coverage: 409205517 bp out of 2315568481 bp ( 17.67 % ) Sampling Time: 00:39:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23870595 Comparison Time: 20:15:47 (hh:mm:ss) Elapsed Time, 187062 HSPs Collected Number of families returned by RECON: 33000 Round Time: 21:16:37 (hh:mm:ss) Elapsed Time : 342 families discovered. RepeatScout/RECON discovery complete: 792 families found Classification Time: 00:30:09 (hh:mm:ss) Elapsed Time Program Time: 26:02:34 (hh:mm:ss) Elapsed Time