RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DxXywe/RM_301557.SatApr121514412025 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: 1744496080 Database = /dev/shm/rModeler.DxXywe/GCA_047715975.1_rBraPum1.hap1 - Sequences = 73 - Bases = 2467904324 Storage Throughput = excellent ( 1675.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024839 bp ( 40024639 non ambiguous ) - Num Contigs Represented = 21 - Sequence extraction : 00:03:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:04 (hh:mm:ss) Elapsed Time Round Time: 00:18:00 (hh:mm:ss) Elapsed Time : 651 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16506 repeats masked totaling 5075739 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000196 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10000196 bp After Masking: 4601341 bp Masked: 53.99 % -- Input Database Coverage: 10000196 bp out of 2467904324 bp ( 0.41 % ) Sampling Time: 00:02:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:38 (hh:mm:ss) Elapsed Time, 32406 HSPs Collected Number of families returned by RECON: 975 Round Time: 00:05:49 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51666 repeats masked totaling 16185988 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024563 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 30024363 bp After Masking: 12441987 bp Masked: 58.56 % -- Input Database Coverage: 40024759 bp out of 2467904324 bp ( 1.62 % ) Sampling Time: 00:09:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:09:31 (hh:mm:ss) Elapsed Time, 32299 HSPs Collected Number of families returned by RECON: 3151 Round Time: 00:19:10 (hh:mm:ss) Elapsed Time : 87 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 164149 repeats masked totaling 49487065 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015444 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 90014244 bp After Masking: 36264415 bp Masked: 59.71 % -- Input Database Coverage: 130040203 bp out of 2467904324 bp ( 5.27 % ) Sampling Time: 00:26:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 00:46:33 (hh:mm:ss) Elapsed Time, 165678 HSPs Collected Number of families returned by RECON: 8707 Round Time: 01:15:34 (hh:mm:ss) Elapsed Time : 322 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:24:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:51:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 533770 repeats masked totaling 158227238 bp(s). - TE Masking time 00:03:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270035726 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 270032726 bp After Masking: 99794500 bp Masked: 63.04 % -- Input Database Coverage: 400075929 bp out of 2467904324 bp ( 16.21 % ) Sampling Time: 01:19:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 04:58:57 (hh:mm:ss) Elapsed Time, 461938 HSPs Collected Number of families returned by RECON: 24569 Round Time: 06:29:07 (hh:mm:ss) Elapsed Time : 872 families discovered. RepeatScout/RECON discovery complete: 1944 families found Classification Time: 00:34:39 (hh:mm:ss) Elapsed Time Program Time: 09:02:19 (hh:mm:ss) Elapsed Time