RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.Wlk51M/RM_1737861.SatJul191540142025 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: 1752964812 Database = /data/tmp/rModeler.Wlk51M/GCA_048593245.1_ASM4859324v1 - Sequences = 6 - Bases = 3066144370 Storage Throughput = excellent ( 2003.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000726 bp ( 40000726 non ambiguous ) - Num Contigs Represented = 6 - Sequence extraction : 00:05:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:44 (hh:mm:ss) Elapsed Time Round Time: 00:20:09 (hh:mm:ss) Elapsed Time : 288 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13977 repeats masked totaling 3232360 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000180 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 10000180 bp After Masking: 6571111 bp Masked: 34.29 % -- Input Database Coverage: 10000180 bp out of 3066144370 bp ( 0.33 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:47 (hh:mm:ss) Elapsed Time, 12762 HSPs Collected Number of families returned by RECON: 1368 Round Time: 00:06:02 (hh:mm:ss) Elapsed Time : 35 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52453 repeats masked totaling 11638562 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000545 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 30000545 bp After Masking: 17903588 bp Masked: 40.32 % -- Input Database Coverage: 40000725 bp out of 3066144370 bp ( 1.30 % ) Sampling Time: 00:05:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:17:14 (hh:mm:ss) Elapsed Time, 29516 HSPs Collected Number of families returned by RECON: 3630 Round Time: 00:23:10 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:38 (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... 172511 repeats masked totaling 38100990 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041518 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 90026226 bp After Masking: 50293487 bp Masked: 44.13 % -- Input Database Coverage: 130042243 bp out of 3066144370 bp ( 4.24 % ) Sampling Time: 00:16:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:39:14 (hh:mm:ss) Elapsed Time, 82223 HSPs Collected Number of families returned by RECON: 10219 Round Time: 01:57:34 (hh:mm:ss) Elapsed Time : 168 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:41:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 574173 repeats masked totaling 122402464 bp(s). - TE Masking time 00:03:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044746 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 270011375 bp After Masking: 142364918 bp Masked: 47.27 % -- Input Database Coverage: 400086989 bp out of 3066144370 bp ( 13.05 % ) Sampling Time: 00:55:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22784625 Comparison Time: 12:33:08 (hh:mm:ss) Elapsed Time, 288879 HSPs Collected Number of families returned by RECON: 39529 Round Time: 13:44:46 (hh:mm:ss) Elapsed Time : 477 families discovered. RepeatScout/RECON discovery complete: 1054 families found Classification Time: 00:20:51 (hh:mm:ss) Elapsed Time Program Time: 16:52:32 (hh:mm:ss) Elapsed Time