RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2xkFnS/RM_6330.SunDec240852372023 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: 1703436757 Database = /dev/shm/rModeler.2xkFnS/GCA_018852605.2_ASM1885260v2 - Sequences = 23 - Bases = 2947873327 Storage Throughput = excellent ( 1204.88 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000793 bp ( 40000793 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:05 (hh:mm:ss) Elapsed Time Round Time: 00:31:57 (hh:mm:ss) Elapsed Time : 243 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (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... 13984 repeats masked totaling 2859219 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000216 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10000216 bp After Masking: 6467960 bp Masked: 35.32 % -- Input Database Coverage: 10000216 bp out of 2947873327 bp ( 0.34 % ) Sampling Time: 00:02:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:13 (hh:mm:ss) Elapsed Time, 6754 HSPs Collected Number of families returned by RECON: 888 Round Time: 00:07:56 (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 : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43707 repeats masked totaling 9160428 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000576 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30000576 bp After Masking: 18567082 bp Masked: 38.11 % -- Input Database Coverage: 40000792 bp out of 2947873327 bp ( 1.36 % ) Sampling Time: 00:07:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:28:07 (hh:mm:ss) Elapsed Time, 33993 HSPs Collected Number of families returned by RECON: 2388 Round Time: 00:42:16 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138855 repeats masked totaling 29893433 bp(s). - TE Masking time 00:01:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90441703 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90001668 bp After Masking: 53439693 bp Masked: 40.62 % -- Input Database Coverage: 130442495 bp out of 2947873327 bp ( 4.42 % ) Sampling Time: 00:20:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 02:59:17 (hh:mm:ss) Elapsed Time, 130406 HSPs Collected Number of families returned by RECON: 7877 Round Time: 03:31:26 (hh:mm:ss) Elapsed Time : 194 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:51:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 458897 repeats masked totaling 99008169 bp(s). - TE Masking time 00:07:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270661104 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 270021076 bp After Masking: 150812374 bp Masked: 44.15 % -- Input Database Coverage: 401103599 bp out of 2947873327 bp ( 13.61 % ) Sampling Time: 01:10:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 22:38:49 (hh:mm:ss) Elapsed Time, 346979 HSPs Collected Number of families returned by RECON: 30886 Round Time: 24:19:29 (hh:mm:ss) Elapsed Time : 425 families discovered. RepeatScout/RECON discovery complete: 946 families found Classification Time: 00:43:02 (hh:mm:ss) Elapsed Time Program Time: 29:56:07 (hh:mm:ss) Elapsed Time