RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5WvJIi/RM_3073602.TueMay161157292023 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: 1684263448 Database = /dev/shm/rModeler.5WvJIi/GCF_027358695.1_aSpeBom1.2.pri - Sequences = 17 - Bases = 987655159 Storage Throughput = good ( 982.87 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40202079 bp ( 40017394 non ambiguous ) - Num Contigs Represented = 13 - Sequence extraction : 00:02:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:04 (hh:mm:ss) Elapsed Time Round Time: 00:30:03 (hh:mm:ss) Elapsed Time : 632 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13193 repeats masked totaling 2274023 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000417 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 10000417 bp After Masking: 7015444 bp Masked: 29.85 % -- Input Database Coverage: 10000417 bp out of 987655159 bp ( 1.01 % ) Sampling Time: 00:02:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:54 (hh:mm:ss) Elapsed Time, 11596 HSPs Collected Number of families returned by RECON: 1213 Round Time: 00:09:44 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43684 repeats masked totaling 7531270 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30201582 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 30016897 bp After Masking: 20265803 bp Masked: 32.49 % -- Input Database Coverage: 40201999 bp out of 987655159 bp ( 4.07 % ) Sampling Time: 00:06:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:32:28 (hh:mm:ss) Elapsed Time, 49763 HSPs Collected Number of families returned by RECON: 3682 Round Time: 00:40:44 (hh:mm:ss) Elapsed Time : 101 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 144683 repeats masked totaling 24573003 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90305084 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 90024642 bp After Masking: 58783104 bp Masked: 34.70 % -- Input Database Coverage: 130507083 bp out of 987655159 bp ( 13.21 % ) Sampling Time: 00:21:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 03:09:02 (hh:mm:ss) Elapsed Time, 257740 HSPs Collected Number of families returned by RECON: 11184 Round Time: 03:38:46 (hh:mm:ss) Elapsed Time : 399 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 488120 repeats masked totaling 84491175 bp(s). - TE Masking time 00:09:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270712560 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 270019582 bp After Masking: 165220822 bp Masked: 38.81 % -- Input Database Coverage: 401219643 bp out of 987655159 bp ( 40.62 % ) Sampling Time: 01:02:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22906296 Comparison Time: 23:00:03 (hh:mm:ss) Elapsed Time, 1594862 HSPs Collected Number of families returned by RECON: 35758 Round Time: 24:51:20 (hh:mm:ss) Elapsed Time : 931 families discovered. RepeatScout/RECON discovery complete: 2089 families found Classification Time: 01:33:12 (hh:mm:ss) Elapsed Time Program Time: 31:23:49 (hh:mm:ss) Elapsed Time