RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.8WEoms/RM_3515023.MonNov270307212023 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: 1701083241 Database = /dev/shm/rModeler.8WEoms/GCF_900634795.4_fBetSpl5.4 - Sequences = 36 - Bases = 427001245 Storage Throughput = good ( 764.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006873 bp ( 40004868 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:54 (hh:mm:ss) Elapsed Time Round Time: 00:19:15 (hh:mm:ss) Elapsed Time : 279 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3652 repeats masked totaling 1151662 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002663 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10001965 bp After Masking: 8516497 bp Masked: 14.85 % -- Input Database Coverage: 10002663 bp out of 427001245 bp ( 2.34 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:44 (hh:mm:ss) Elapsed Time, 5565 HSPs Collected Number of families returned by RECON: 518 Round Time: 00:07:07 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11604 repeats masked totaling 3543145 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004130 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30002823 bp After Masking: 25506674 bp Masked: 14.99 % -- Input Database Coverage: 40006793 bp out of 427001245 bp ( 9.37 % ) Sampling Time: 00:02:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:27:28 (hh:mm:ss) Elapsed Time, 15809 HSPs Collected Number of families returned by RECON: 2710 Round Time: 00:30:20 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31842 repeats masked totaling 9945442 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045287 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90037860 bp After Masking: 76929523 bp Masked: 14.56 % -- Input Database Coverage: 130052080 bp out of 427001245 bp ( 30.46 % ) Sampling Time: 00:07:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 03:03:07 (hh:mm:ss) Elapsed Time, 115365 HSPs Collected Number of families returned by RECON: 12451 Round Time: 03:14:55 (hh:mm:ss) Elapsed Time : 196 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 124100 repeats masked totaling 38223249 bp(s). - TE Masking time 00:05:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270026042 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 270006638 bp After Masking: 222819493 bp Masked: 17.48 % -- Input Database Coverage: 400078122 bp out of 427001245 bp ( 93.69 % ) Sampling Time: 00:22:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 23:01:01 (hh:mm:ss) Elapsed Time, 491779 HSPs Collected Number of families returned by RECON: 61892 Round Time: 24:18:14 (hh:mm:ss) Elapsed Time : 516 families discovered. RepeatScout/RECON discovery complete: 1018 families found Classification Time: 01:03:13 (hh:mm:ss) Elapsed Time Program Time: 29:33:04 (hh:mm:ss) Elapsed Time