RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.olkdih/RM_3148174.WedNov132134502024 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: 1731562490 Database = /scratch/tmp/rModeler.olkdih/GCF_037176765.1_rAnoSag1.mat - Sequences = 29 - Bases = 1950830970 Storage Throughput = excellent ( 1448.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002270 bp ( 40001470 non ambiguous ) - Num Contigs Represented = 16 - Sequence extraction : 00:02:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:33 (hh:mm:ss) Elapsed Time Round Time: 00:11:57 (hh:mm:ss) Elapsed Time : 674 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21556 repeats masked totaling 4187089 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000488 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 10000288 bp After Masking: 5514980 bp Masked: 44.85 % -- Input Database Coverage: 10000488 bp out of 1950830970 bp ( 0.51 % ) Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:05 (hh:mm:ss) Elapsed Time, 8871 HSPs Collected Number of families returned by RECON: 1137 Round Time: 00:04:17 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68242 repeats masked totaling 12793456 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001702 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 30001102 bp After Masking: 15832059 bp Masked: 47.23 % -- Input Database Coverage: 40002190 bp out of 1950830970 bp ( 2.05 % ) Sampling Time: 00:03:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:12:31 (hh:mm:ss) Elapsed Time, 38356 HSPs Collected Number of families returned by RECON: 3513 Round Time: 00:16:22 (hh:mm:ss) Elapsed Time : 110 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 222122 repeats masked totaling 41083594 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039742 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 90037142 bp After Masking: 44975407 bp Masked: 50.05 % -- Input Database Coverage: 130041932 bp out of 1950830970 bp ( 6.67 % ) Sampling Time: 00:09:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:08:59 (hh:mm:ss) Elapsed Time, 162898 HSPs Collected Number of families returned by RECON: 9802 Round Time: 01:22:25 (hh:mm:ss) Elapsed Time : 366 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 734200 repeats masked totaling 131815920 bp(s). - TE Masking time 00:03:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270018357 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 270014888 bp After Masking: 126406315 bp Masked: 53.19 % -- Input Database Coverage: 400060289 bp out of 1950830970 bp ( 20.51 % ) Sampling Time: 00:30:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22784625 Comparison Time: 08:12:51 (hh:mm:ss) Elapsed Time, 428096 HSPs Collected Number of families returned by RECON: 32584 Round Time: 08:58:49 (hh:mm:ss) Elapsed Time : 880 families discovered. RepeatScout/RECON discovery complete: 2059 families found Classification Time: 00:31:29 (hh:mm:ss) Elapsed Time Program Time: 11:25:19 (hh:mm:ss) Elapsed Time