RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FeVbtA/RM_362686.SatJan141258462023 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: 1673729925 Database = /dev/shm/rModeler.FeVbtA/GCA_944039275.1_fDanRer4.1 - Sequences = 73 - Bases = 1413675870 Storage Throughput = good ( 986.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014986 bp ( 40009286 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:56 (hh:mm:ss) Elapsed Time Round Time: 00:27:55 (hh:mm:ss) Elapsed Time : 1093 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20923 repeats masked totaling 4104048 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003450 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10001550 bp After Masking: 5151238 bp Masked: 48.50 % -- Input Database Coverage: 10003450 bp out of 1413675870 bp ( 0.71 % ) Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:58 (hh:mm:ss) Elapsed Time, 7348 HSPs Collected Number of families returned by RECON: 1274 Round Time: 00:07:59 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64533 repeats masked totaling 12703880 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011456 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30007656 bp After Masking: 15029241 bp Masked: 49.92 % -- Input Database Coverage: 40014906 bp out of 1413675870 bp ( 2.83 % ) Sampling Time: 00:04:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:25:16 (hh:mm:ss) Elapsed Time, 47607 HSPs Collected Number of families returned by RECON: 4107 Round Time: 00:31:15 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 204051 repeats masked totaling 39187781 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020049 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 90013832 bp After Masking: 43227003 bp Masked: 51.98 % -- Input Database Coverage: 130034955 bp out of 1413675870 bp ( 9.20 % ) Sampling Time: 00:17:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 02:02:41 (hh:mm:ss) Elapsed Time, 281955 HSPs Collected Number of families returned by RECON: 11187 Round Time: 02:27:15 (hh:mm:ss) Elapsed Time : 578 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 680472 repeats masked totaling 131851059 bp(s). - TE Masking time 00:10:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270059287 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 270033387 bp After Masking: 116004788 bp Masked: 57.04 % -- Input Database Coverage: 400094242 bp out of 1413675870 bp ( 28.30 % ) Sampling Time: 00:48:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 11:59:17 (hh:mm:ss) Elapsed Time, 691687 HSPs Collected Number of families returned by RECON: 31667 Round Time: 13:17:24 (hh:mm:ss) Elapsed Time : 1240 families discovered. RepeatScout/RECON discovery complete: 3069 families found Classification Time: 01:21:37 (hh:mm:ss) Elapsed Time Program Time: 18:13:25 (hh:mm:ss) Elapsed Time