RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.b8sHN4/RM_2509612.SatMar91753362024 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: 1710035614 Database = /dev/shm/rModeler.b8sHN4/GCA_023053635.2_rElgMul1.1.pri - Sequences = 35 - Bases = 1790519499 Storage Throughput = excellent ( 1225.41 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015032 bp ( 40014932 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:02:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:11 (hh:mm:ss) Elapsed Time Round Time: 00:23:46 (hh:mm:ss) Elapsed Time : 628 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21218 repeats masked totaling 3637337 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000531 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10000531 bp After Masking: 6191942 bp Masked: 38.08 % -- Input Database Coverage: 10000531 bp out of 1790519499 bp ( 0.56 % ) Sampling Time: 00:01:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:25 (hh:mm:ss) Elapsed Time, 13013 HSPs Collected Number of families returned by RECON: 1523 Round Time: 00:07:02 (hh:mm:ss) Elapsed Time : 40 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67142 repeats masked totaling 11170053 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014488 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30014388 bp After Masking: 17876484 bp Masked: 40.44 % -- Input Database Coverage: 40015019 bp out of 1790519499 bp ( 2.23 % ) Sampling Time: 00:04:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:24:46 (hh:mm:ss) Elapsed Time, 61737 HSPs Collected Number of families returned by RECON: 4461 Round Time: 00:31:04 (hh:mm:ss) Elapsed Time : 133 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 220663 repeats masked totaling 36372118 bp(s). - TE Masking time 00:01:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022295 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90021695 bp After Masking: 51386777 bp Masked: 42.92 % -- Input Database Coverage: 130037314 bp out of 1790519499 bp ( 7.26 % ) Sampling Time: 00:12:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 02:27:17 (hh:mm:ss) Elapsed Time, 226356 HSPs Collected Number of families returned by RECON: 13436 Round Time: 02:47:30 (hh:mm:ss) Elapsed Time : 471 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 732127 repeats masked totaling 121689260 bp(s). - TE Masking time 00:08:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041709 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270039309 bp After Masking: 141778342 bp Masked: 47.50 % -- Input Database Coverage: 400079023 bp out of 1790519499 bp ( 22.34 % ) Sampling Time: 00:38:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 16:48:21 (hh:mm:ss) Elapsed Time, 585875 HSPs Collected Number of families returned by RECON: 43832 Round Time: 18:26:30 (hh:mm:ss) Elapsed Time : 1102 families discovered. RepeatScout/RECON discovery complete: 2374 families found Classification Time: 01:13:35 (hh:mm:ss) Elapsed Time Program Time: 23:29:27 (hh:mm:ss) Elapsed Time