RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.YbNHSk/RM_3234548.ThuApr170614312025 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: 1744895670 Database = /dev/shm/rModeler.YbNHSk/GCA_965140255.1_rLepOli2.hap2 - Sequences = 40 - Bases = 2208046144 Storage Throughput = excellent ( 1700.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024767 bp ( 40024466 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:46 (hh:mm:ss) Elapsed Time Round Time: 00:13:14 (hh:mm:ss) Elapsed Time : 516 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13455 repeats masked totaling 2987437 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000218 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10000218 bp After Masking: 6898597 bp Masked: 31.02 % -- Input Database Coverage: 10000218 bp out of 2208046144 bp ( 0.45 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:58 (hh:mm:ss) Elapsed Time, 11091 HSPs Collected Number of families returned by RECON: 1589 Round Time: 00:03:51 (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 : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43442 repeats masked totaling 9512294 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024469 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30024168 bp After Masking: 20112892 bp Masked: 33.01 % -- Input Database Coverage: 40024687 bp out of 2208046144 bp ( 1.81 % ) Sampling Time: 00:02:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:26 (hh:mm:ss) Elapsed Time, 72287 HSPs Collected Number of families returned by RECON: 4940 Round Time: 00:16:01 (hh:mm:ss) Elapsed Time : 160 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 151867 repeats masked totaling 33189303 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045275 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90004775 bp After Masking: 55386459 bp Masked: 38.46 % -- Input Database Coverage: 130069962 bp out of 2208046144 bp ( 5.89 % ) Sampling Time: 00:06:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:05:23 (hh:mm:ss) Elapsed Time, 223485 HSPs Collected Number of families returned by RECON: 13475 Round Time: 01:15:26 (hh:mm:ss) Elapsed Time : 421 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 519402 repeats masked totaling 112259414 bp(s). - TE Masking time 00:03:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270068645 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 270015602 bp After Masking: 153434276 bp Masked: 43.18 % -- Input Database Coverage: 400138607 bp out of 2208046144 bp ( 18.12 % ) Sampling Time: 00:20:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 07:03:32 (hh:mm:ss) Elapsed Time, 549996 HSPs Collected Number of families returned by RECON: 43155 Round Time: 07:46:47 (hh:mm:ss) Elapsed Time : 1013 families discovered. RepeatScout/RECON discovery complete: 2136 families found Classification Time: 00:39:39 (hh:mm:ss) Elapsed Time Program Time: 10:14:58 (hh:mm:ss) Elapsed Time