RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wwHLPb/RM_18221.SatJul271300002024 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: 1722110398 Database = /dev/shm/rModeler.wwHLPb/GCF_020085105.1_ASM2008510v1 - Sequences = 65 - Bases = 718820513 Storage Throughput = excellent ( 1181.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029728 bp ( 40028928 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:27 (hh:mm:ss) Elapsed Time Round Time: 00:27:03 (hh:mm:ss) Elapsed Time : 634 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11652 repeats masked totaling 1591189 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004147 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10003947 bp After Masking: 8243362 bp Masked: 17.60 % -- Input Database Coverage: 10004147 bp out of 718820513 bp ( 1.39 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:08:40 (hh:mm:ss) Elapsed Time, 8415 HSPs Collected Number of families returned by RECON: 1844 Round Time: 00:10:12 (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 : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36328 repeats masked totaling 4994684 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025567 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30024967 bp After Masking: 24418742 bp Masked: 18.67 % -- Input Database Coverage: 40029714 bp out of 718820513 bp ( 5.57 % ) Sampling Time: 00:03:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:42:08 (hh:mm:ss) Elapsed Time, 59064 HSPs Collected Number of families returned by RECON: 6236 Round Time: 00:49:33 (hh:mm:ss) Elapsed Time : 142 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 122346 repeats masked totaling 17626523 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013315 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90012515 bp After Masking: 70642770 bp Masked: 21.52 % -- Input Database Coverage: 130043029 bp out of 718820513 bp ( 18.09 % ) Sampling Time: 00:10:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 04:23:29 (hh:mm:ss) Elapsed Time, 328256 HSPs Collected Number of families returned by RECON: 21365 Round Time: 04:54:40 (hh:mm:ss) Elapsed Time : 634 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 451796 repeats masked totaling 68237260 bp(s). - TE Masking time 00:12:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270026045 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 270023245 bp After Masking: 196686369 bp Masked: 27.16 % -- Input Database Coverage: 400069074 bp out of 718820513 bp ( 55.66 % ) Sampling Time: 00:41:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22885995 Comparison Time: 30:01:09 (hh:mm:ss) Elapsed Time, 858940 HSPs Collected Number of families returned by RECON: 74050 Round Time: 33:24:50 (hh:mm:ss) Elapsed Time : 1412 families discovered. RepeatScout/RECON discovery complete: 2840 families found Classification Time: 01:45:32 (hh:mm:ss) Elapsed Time Program Time: 41:31:50 (hh:mm:ss) Elapsed Time