RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.hABRkH/RM_1855804.TueApr220817012025 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: 1745335020 Database = /dev/shm/rModeler.hABRkH/GCA_965152235.1_rEreImb1.hap1 - Sequences = 57 - Bases = 2218003986 Storage Throughput = excellent ( 1819.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036967 bp ( 40013818 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:12 (hh:mm:ss) Elapsed Time Round Time: 00:11:30 (hh:mm:ss) Elapsed Time : 534 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13336 repeats masked totaling 3064094 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000811 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10000811 bp After Masking: 6843566 bp Masked: 31.57 % -- Input Database Coverage: 10000811 bp out of 2218003986 bp ( 0.45 % ) Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:17 (hh:mm:ss) Elapsed Time, 15161 HSPs Collected Number of families returned by RECON: 1639 Round Time: 00:04:26 (hh:mm:ss) Elapsed Time : 38 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45068 repeats masked totaling 9755734 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036076 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30012927 bp After Masking: 20022218 bp Masked: 33.29 % -- Input Database Coverage: 40036887 bp out of 2218003986 bp ( 1.81 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:10 (hh:mm:ss) Elapsed Time, 97992 HSPs Collected Number of families returned by RECON: 4580 Round Time: 00:14:59 (hh:mm:ss) Elapsed Time : 127 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 154597 repeats masked totaling 32394257 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009430 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90005389 bp After Masking: 56983849 bp Masked: 36.69 % -- Input Database Coverage: 130046317 bp out of 2218003986 bp ( 5.86 % ) Sampling Time: 00:05:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:10:30 (hh:mm:ss) Elapsed Time, 508375 HSPs Collected Number of families returned by RECON: 14040 Round Time: 01:20:24 (hh:mm:ss) Elapsed Time : 462 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 536129 repeats masked totaling 112994413 bp(s). - TE Masking time 00:03:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270358886 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 270008774 bp After Masking: 154883972 bp Masked: 42.64 % -- Input Database Coverage: 400405203 bp out of 2218003986 bp ( 18.05 % ) Sampling Time: 00:20:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22865703 Comparison Time: 07:54:44 (hh:mm:ss) Elapsed Time, 2626657 HSPs Collected Number of families returned by RECON: 43317 Round Time: 08:38:18 (hh:mm:ss) Elapsed Time : 979 families discovered. RepeatScout/RECON discovery complete: 2140 families found Classification Time: 00:42:14 (hh:mm:ss) Elapsed Time Program Time: 11:11:51 (hh:mm:ss) Elapsed Time