RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3vVIMj/RM_47217.FriDec301411462022 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: 1672438306 Database = /dev/shm/rModeler.3vVIMj/GCA_910589615.1_fTauBub2.1 - Sequences = 27 - Bases = 615153901 Storage Throughput = excellent ( 1167.70 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028721 bp ( 40023921 non ambiguous ) - Num Contigs Represented = 21 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:39 (hh:mm:ss) Elapsed Time Round Time: 00:19:31 (hh:mm:ss) Elapsed Time : 454 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6070 repeats masked totaling 1034826 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001908 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10000608 bp After Masking: 8161755 bp Masked: 18.39 % -- Input Database Coverage: 10001908 bp out of 615153901 bp ( 1.63 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:20 (hh:mm:ss) Elapsed Time, 7002 HSPs Collected Number of families returned by RECON: 1352 Round Time: 00:07:13 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18787 repeats masked totaling 2986701 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026799 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 30023299 bp After Masking: 24473244 bp Masked: 18.49 % -- Input Database Coverage: 40028707 bp out of 615153901 bp ( 6.51 % ) Sampling Time: 00:05:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:28:49 (hh:mm:ss) Elapsed Time, 44718 HSPs Collected Number of families returned by RECON: 5022 Round Time: 00:35:21 (hh:mm:ss) Elapsed Time : 84 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68005 repeats masked totaling 10689071 bp(s). - TE Masking time 00:01:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035109 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 90021309 bp After Masking: 71791808 bp Masked: 20.25 % -- Input Database Coverage: 130063816 bp out of 615153901 bp ( 21.14 % ) Sampling Time: 00:17:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 03:29:28 (hh:mm:ss) Elapsed Time, 233788 HSPs Collected Number of families returned by RECON: 17692 Round Time: 03:56:41 (hh:mm:ss) Elapsed Time : 410 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 259029 repeats masked totaling 41707292 bp(s). - TE Masking time 00:06:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270059684 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270026484 bp After Masking: 204941466 bp Masked: 24.10 % -- Input Database Coverage: 400123500 bp out of 615153901 bp ( 65.04 % ) Sampling Time: 00:57:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 25:00:40 (hh:mm:ss) Elapsed Time, 759954 HSPs Collected Number of families returned by RECON: 65737 Round Time: 27:20:58 (hh:mm:ss) Elapsed Time : 1035 families discovered. RepeatScout/RECON discovery complete: 1996 families found Classification Time: 01:15:39 (hh:mm:ss) Elapsed Time Program Time: 33:35:23 (hh:mm:ss) Elapsed Time