RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ZcSe0w/RM_74269.SunJan152226552023 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: 1673850413 Database = /dev/shm/rModeler.ZcSe0w/GCF_004126475.2_mPhyDis1.pri.v3 - Sequences = 77 - Bases = 2108832841 Storage Throughput = good ( 949.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40325235 bp ( 40032746 non ambiguous ) - Num Contigs Represented = 20 - Sequence extraction : 00:04:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:12 (hh:mm:ss) Elapsed Time Round Time: 00:31:29 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8045 repeats masked totaling 2215506 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10044222 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 10021716 bp After Masking: 7745640 bp Masked: 22.71 % -- Input Database Coverage: 10044222 bp out of 2108832841 bp ( 0.48 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:13:38 (hh:mm:ss) Elapsed Time, 5130 HSPs Collected Number of families returned by RECON: 871 Round Time: 00:15:38 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27553 repeats masked totaling 7419816 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30280933 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 30010950 bp After Masking: 22484187 bp Masked: 25.08 % -- Input Database Coverage: 40325155 bp out of 2108832841 bp ( 1.91 % ) Sampling Time: 00:04:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:30:24 (hh:mm:ss) Elapsed Time, 26065 HSPs Collected Number of families returned by RECON: 2621 Round Time: 00:36:22 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:10:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 93729 repeats masked totaling 25232915 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90698271 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90001164 bp After Masking: 64426185 bp Masked: 28.42 % -- Input Database Coverage: 131023426 bp out of 2108832841 bp ( 6.21 % ) Sampling Time: 00:14:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 03:01:56 (hh:mm:ss) Elapsed Time, 77842 HSPs Collected Number of families returned by RECON: 8692 Round Time: 03:20:16 (hh:mm:ss) Elapsed Time : 162 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 312803 repeats masked totaling 80709354 bp(s). - TE Masking time 00:04:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272230849 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 270026027 bp After Masking: 188422906 bp Masked: 30.22 % -- Input Database Coverage: 403254275 bp out of 2108832841 bp ( 19.12 % ) Sampling Time: 00:36:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23184645 Comparison Time: 20:05:43 (hh:mm:ss) Elapsed Time, 236427 HSPs Collected Number of families returned by RECON: 37986 Round Time: 21:03:09 (hh:mm:ss) Elapsed Time : 376 families discovered. RepeatScout/RECON discovery complete: 826 families found Classification Time: 00:28:05 (hh:mm:ss) Elapsed Time Program Time: 26:14:59 (hh:mm:ss) Elapsed Time