RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3fKz3p/RM_1907097.MonJan151108182024 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: 1705345697 Database = /dev/shm/rModeler.3fKz3p/GCA_963277665.1_drVisAlbu1.1 - Sequences = 6 - Bases = 10824455427 Storage Throughput = excellent ( 1065.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039920 bp ( 40039720 non ambiguous ) - Num Contigs Represented = 6 - Sequence extraction : 00:40:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:29 (hh:mm:ss) Elapsed Time Round Time: 01:21:30 (hh:mm:ss) Elapsed Time : 419 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:11:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8583 repeats masked totaling 5832660 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 9999920 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 9999920 bp After Masking: 4041374 bp Masked: 59.59 % -- Input Database Coverage: 9999920 bp out of 10824455427 bp ( 0.09 % ) Sampling Time: 00:12:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:10:30 (hh:mm:ss) Elapsed Time, 7452 HSPs Collected Number of families returned by RECON: 823 Round Time: 00:23:58 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:30:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27079 repeats masked totaling 18472408 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039920 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 30039720 bp After Masking: 11261835 bp Masked: 62.51 % -- Input Database Coverage: 40039840 bp out of 10824455427 bp ( 0.37 % ) Sampling Time: 00:34:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:45:36 (hh:mm:ss) Elapsed Time, 32595 HSPs Collected Number of families returned by RECON: 2611 Round Time: 01:21:10 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 01:30:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 85783 repeats masked totaling 57673456 bp(s). - TE Masking time 00:04:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039920 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 90038920 bp After Masking: 31260948 bp Masked: 65.28 % -- Input Database Coverage: 130079760 bp out of 10824455427 bp ( 1.20 % ) Sampling Time: 01:41:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 03:56:10 (hh:mm:ss) Elapsed Time, 242604 HSPs Collected Number of families returned by RECON: 7514 Round Time: 05:48:22 (hh:mm:ss) Elapsed Time : 242 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 04:33:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 299360 repeats masked totaling 196829872 bp(s). - TE Masking time 00:23:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039920 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 270037350 bp After Masking: 69900543 bp Masked: 74.11 % -- Input Database Coverage: 400119680 bp out of 10824455427 bp ( 3.70 % ) Sampling Time: 05:17:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22784625 Comparison Time: 18:44:36 (hh:mm:ss) Elapsed Time, 583659 HSPs Collected Number of families returned by RECON: 18355 Round Time: 24:33:16 (hh:mm:ss) Elapsed Time : 602 families discovered. RepeatScout/RECON discovery complete: 1316 families found Classification Time: 01:36:44 (hh:mm:ss) Elapsed Time Program Time: 35:05:00 (hh:mm:ss) Elapsed Time