RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.Ehkk6T/RM_269316.WedDec112006382024 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: 1733976397 Database = /data/tmp/rModeler.Ehkk6T/GCF_018350175.1_F.catus_Fca126_mat1.0 - Sequences = 71 - Bases = 2425747038 Storage Throughput = fair ( 682.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001068 bp ( 40000968 non ambiguous ) - Num Contigs Represented = 21 - Sequence extraction : 00:02:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:00 (hh:mm:ss) Elapsed Time Round Time: 00:18:11 (hh:mm:ss) Elapsed Time : 181 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10047 repeats masked totaling 2333581 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000288 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10000188 bp After Masking: 7561139 bp Masked: 24.39 % -- Input Database Coverage: 10000288 bp out of 2425747038 bp ( 0.41 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:07 (hh:mm:ss) Elapsed Time, 8066 HSPs Collected Number of families returned by RECON: 972 Round Time: 00:05:36 (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 : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36063 repeats masked totaling 8060386 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000700 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 30000700 bp After Masking: 21638528 bp Masked: 27.87 % -- Input Database Coverage: 40000988 bp out of 2425747038 bp ( 1.65 % ) Sampling Time: 00:02:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:18:41 (hh:mm:ss) Elapsed Time, 26161 HSPs Collected Number of families returned by RECON: 2280 Round Time: 00:22:30 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 114338 repeats masked totaling 26142404 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038044 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90037044 bp After Masking: 63054356 bp Masked: 29.97 % -- Input Database Coverage: 130039032 bp out of 2425747038 bp ( 5.36 % ) Sampling Time: 00:09:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 01:56:30 (hh:mm:ss) Elapsed Time, 69224 HSPs Collected Number of families returned by RECON: 8461 Round Time: 02:08:28 (hh:mm:ss) Elapsed Time : 152 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 381495 repeats masked totaling 86050986 bp(s). - TE Masking time 00:02:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034427 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 270034327 bp After Masking: 181159041 bp Masked: 32.91 % -- Input Database Coverage: 400073459 bp out of 2425747038 bp ( 16.49 % ) Sampling Time: 00:24:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 13:38:11 (hh:mm:ss) Elapsed Time, 202667 HSPs Collected Number of families returned by RECON: 35690 Round Time: 14:32:09 (hh:mm:ss) Elapsed Time : 366 families discovered. RepeatScout/RECON discovery complete: 790 families found Classification Time: 00:20:24 (hh:mm:ss) Elapsed Time Program Time: 17:47:18 (hh:mm:ss) Elapsed Time