RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.twOk5n/RM_3225407.MonApr11407352024 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: 1712005653 Database = /dev/shm/rModeler.twOk5n/GCF_027574615.1_DD_ASM_mEF_20220401 - Sequences = 48 - Bases = 2008057866 Storage Throughput = excellent ( 1183.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038771 bp ( 40038272 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:30 (hh:mm:ss) Elapsed Time Round Time: 00:24:20 (hh:mm:ss) Elapsed Time : 354 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15573 repeats masked totaling 2845621 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000785 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10000785 bp After Masking: 6931595 bp Masked: 30.69 % -- Input Database Coverage: 10000785 bp out of 2008057866 bp ( 0.50 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:08:30 (hh:mm:ss) Elapsed Time, 6627 HSPs Collected Number of families returned by RECON: 768 Round Time: 00:10:18 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48169 repeats masked totaling 8446446 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037980 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30037481 bp After Masking: 20915514 bp Masked: 30.37 % -- Input Database Coverage: 40038765 bp out of 2008057866 bp ( 1.99 % ) Sampling Time: 00:03:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:35:04 (hh:mm:ss) Elapsed Time, 23234 HSPs Collected Number of families returned by RECON: 2485 Round Time: 00:39:40 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157355 repeats masked totaling 28276146 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024220 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90023008 bp After Masking: 59761139 bp Masked: 33.62 % -- Input Database Coverage: 130062985 bp out of 2008057866 bp ( 6.48 % ) Sampling Time: 00:10:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 03:06:20 (hh:mm:ss) Elapsed Time, 102234 HSPs Collected Number of families returned by RECON: 8757 Round Time: 03:19:53 (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 : 00:12:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 502832 repeats masked totaling 92758506 bp(s). - TE Masking time 00:05:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270033716 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 270027802 bp After Masking: 170683306 bp Masked: 36.79 % -- Input Database Coverage: 400096701 bp out of 2008057866 bp ( 19.92 % ) Sampling Time: 00:33:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22825146 Comparison Time: 21:20:30 (hh:mm:ss) Elapsed Time, 240138 HSPs Collected Number of families returned by RECON: 34002 Round Time: 22:15:18 (hh:mm:ss) Elapsed Time : 442 families discovered. RepeatScout/RECON discovery complete: 1065 families found Classification Time: 00:35:28 (hh:mm:ss) Elapsed Time Program Time: 27:24:57 (hh:mm:ss) Elapsed Time