RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Cc8NDg/RM_15781.SunDec240852592023 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: 1703436771 Database = /dev/shm/rModeler.Cc8NDg/GCA_018852615.2_ASM1885261v2 - Sequences = 24 - Bases = 3051542087 Storage Throughput = excellent ( 1161.27 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40360760 bp ( 40000727 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:03 (hh:mm:ss) Elapsed Time Round Time: 00:31:13 (hh:mm:ss) Elapsed Time : 269 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16610 repeats masked totaling 3140099 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10120094 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10000088 bp After Masking: 6421248 bp Masked: 35.79 % -- Input Database Coverage: 10120094 bp out of 3051542087 bp ( 0.33 % ) Sampling Time: 00:02:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:18 (hh:mm:ss) Elapsed Time, 7643 HSPs Collected Number of families returned by RECON: 884 Round Time: 00:08:03 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49950 repeats masked totaling 9458045 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30240586 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30000559 bp After Masking: 18602485 bp Masked: 37.99 % -- Input Database Coverage: 40360680 bp out of 3051542087 bp ( 1.32 % ) Sampling Time: 00:05:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:26:48 (hh:mm:ss) Elapsed Time, 25166 HSPs Collected Number of families returned by RECON: 2309 Round Time: 00:33:35 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 167033 repeats masked totaling 31598137 bp(s). - TE Masking time 00:01:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90641544 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90018368 bp After Masking: 52709545 bp Masked: 41.45 % -- Input Database Coverage: 131002224 bp out of 3051542087 bp ( 4.29 % ) Sampling Time: 00:24:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 02:57:49 (hh:mm:ss) Elapsed Time, 96621 HSPs Collected Number of families returned by RECON: 7681 Round Time: 03:26:25 (hh:mm:ss) Elapsed Time : 189 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:44:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 528587 repeats masked totaling 102316371 bp(s). - TE Masking time 00:07:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272361963 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 270031245 bp After Masking: 151233014 bp Masked: 43.99 % -- Input Database Coverage: 403364187 bp out of 3051542087 bp ( 13.22 % ) Sampling Time: 01:05:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23177836 Comparison Time: 22:52:17 (hh:mm:ss) Elapsed Time, 262886 HSPs Collected Number of families returned by RECON: 30928 Round Time: 24:22:05 (hh:mm:ss) Elapsed Time : 370 families discovered. RepeatScout/RECON discovery complete: 920 families found Classification Time: 00:39:36 (hh:mm:ss) Elapsed Time Program Time: 29:40:57 (hh:mm:ss) Elapsed Time