RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.kvjxYO/RM_405742.WedMay101031142023 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: 1683739873 Database = /dev/shm/rModeler.kvjxYO/GCA_027579695.1_fNeoGra1.pri - Sequences = 38 - Bases = 2341916362 Storage Throughput = excellent ( 1343.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40203316 bp ( 40014941 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:36 (hh:mm:ss) Elapsed Time Round Time: 00:24:22 (hh:mm:ss) Elapsed Time : 933 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18107 repeats masked totaling 5567411 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10080495 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10019433 bp After Masking: 4014916 bp Masked: 59.93 % -- Input Database Coverage: 10080495 bp out of 2341916362 bp ( 0.43 % ) Sampling Time: 00:03:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:06 (hh:mm:ss) Elapsed Time, 13909 HSPs Collected Number of families returned by RECON: 1224 Round Time: 00:10:00 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53838 repeats masked totaling 17196942 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30162826 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30035513 bp After Masking: 11544286 bp Masked: 61.56 % -- Input Database Coverage: 40243321 bp out of 2341916362 bp ( 1.72 % ) Sampling Time: 00:06:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:23:49 (hh:mm:ss) Elapsed Time, 46534 HSPs Collected Number of families returned by RECON: 4006 Round Time: 00:31:50 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 168936 repeats masked totaling 52253872 bp(s). - TE Masking time 00:02:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90611451 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 90000585 bp After Masking: 33922151 bp Masked: 62.31 % -- Input Database Coverage: 130854772 bp out of 2341916362 bp ( 5.59 % ) Sampling Time: 00:20:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 02:02:47 (hh:mm:ss) Elapsed Time, 307466 HSPs Collected Number of families returned by RECON: 10882 Round Time: 02:34:06 (hh:mm:ss) Elapsed Time : 549 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 571147 repeats masked totaling 173437223 bp(s). - TE Masking time 00:14:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271525401 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 270031240 bp After Masking: 85105924 bp Masked: 68.48 % -- Input Database Coverage: 402380173 bp out of 2341916362 bp ( 17.18 % ) Sampling Time: 01:15:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 12:07:17 (hh:mm:ss) Elapsed Time, 875580 HSPs Collected Number of families returned by RECON: 27165 Round Time: 14:11:09 (hh:mm:ss) Elapsed Time : 1301 families discovered. RepeatScout/RECON discovery complete: 2865 families found Classification Time: 02:45:08 (hh:mm:ss) Elapsed Time Program Time: 20:36:35 (hh:mm:ss) Elapsed Time