RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.XecjoA/RM_261619.SunNov171250062024 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: 1731876606 Database = /scratch/tmp/rModeler.XecjoA/GCA_964188405.1_fProPar1.1 - Sequences = 24 - Bases = 1235328005 Storage Throughput = excellent ( 1574.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40043985 bp ( 40025630 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:51 (hh:mm:ss) Elapsed Time Round Time: 00:14:56 (hh:mm:ss) Elapsed Time : 1168 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22917 repeats masked totaling 3043851 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041021 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10035421 bp After Masking: 5336131 bp Masked: 46.83 % -- Input Database Coverage: 10041021 bp out of 1235328005 bp ( 0.81 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:59 (hh:mm:ss) Elapsed Time, 21899 HSPs Collected Number of families returned by RECON: 1646 Round Time: 00:04:50 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71242 repeats masked totaling 9417248 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042948 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30030193 bp After Masking: 16071331 bp Masked: 46.48 % -- Input Database Coverage: 40083969 bp out of 1235328005 bp ( 3.24 % ) Sampling Time: 00:04:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:38 (hh:mm:ss) Elapsed Time, 52952 HSPs Collected Number of families returned by RECON: 6074 Round Time: 00:17:43 (hh:mm:ss) Elapsed Time : 131 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 225844 repeats masked totaling 28957669 bp(s). - TE Masking time 00:01:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90049556 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90012115 bp After Masking: 47547839 bp Masked: 47.18 % -- Input Database Coverage: 130133525 bp out of 1235328005 bp ( 10.53 % ) Sampling Time: 00:12:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:08:26 (hh:mm:ss) Elapsed Time, 399811 HSPs Collected Number of families returned by RECON: 18343 Round Time: 01:29:04 (hh:mm:ss) Elapsed Time : 798 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 785319 repeats masked totaling 104713993 bp(s). - TE Masking time 00:06:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270119801 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 270004013 bp After Masking: 125286567 bp Masked: 53.60 % -- Input Database Coverage: 400253326 bp out of 1235328005 bp ( 32.40 % ) Sampling Time: 00:38:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 07:21:46 (hh:mm:ss) Elapsed Time, 1460051 HSPs Collected Number of families returned by RECON: 53421 Round Time: 08:45:57 (hh:mm:ss) Elapsed Time : 1748 families discovered. RepeatScout/RECON discovery complete: 3863 families found Classification Time: 01:03:41 (hh:mm:ss) Elapsed Time Program Time: 11:56:11 (hh:mm:ss) Elapsed Time