RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.R7YfOz/RM_31092.SatDec311118012022 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: 1672514281 Database = /dev/shm/rModeler.R7YfOz/GCA_020745685.1_fTauAds1.pri.cur - Sequences = 64 - Bases = 723582185 Storage Throughput = excellent ( 1027.76 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40368345 bp ( 40017559 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:53 (hh:mm:ss) Elapsed Time Round Time: 00:25:17 (hh:mm:ss) Elapsed Time : 540 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8677 repeats masked totaling 1520853 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10081851 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10019688 bp After Masking: 8022960 bp Masked: 19.93 % -- Input Database Coverage: 10081851 bp out of 723582185 bp ( 1.39 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:21 (hh:mm:ss) Elapsed Time, 6116 HSPs Collected Number of families returned by RECON: 1179 Round Time: 00:08:10 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27608 repeats masked totaling 4907504 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30326349 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30037726 bp After Masking: 23815598 bp Masked: 20.71 % -- Input Database Coverage: 40408200 bp out of 723582185 bp ( 5.58 % ) Sampling Time: 00:04:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:33:37 (hh:mm:ss) Elapsed Time, 39535 HSPs Collected Number of families returned by RECON: 4545 Round Time: 00:39:34 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 92018 repeats masked totaling 16345642 bp(s). - TE Masking time 00:01:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90510502 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 90023811 bp After Masking: 69664372 bp Masked: 22.62 % -- Input Database Coverage: 130918702 bp out of 723582185 bp ( 18.09 % ) Sampling Time: 00:11:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 03:54:28 (hh:mm:ss) Elapsed Time, 205783 HSPs Collected Number of families returned by RECON: 15755 Round Time: 04:17:00 (hh:mm:ss) Elapsed Time : 448 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 328133 repeats masked totaling 58844070 bp(s). - TE Masking time 00:10:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271524086 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 270001758 bp After Masking: 199834599 bp Masked: 25.99 % -- Input Database Coverage: 402442788 bp out of 723582185 bp ( 55.62 % ) Sampling Time: 00:38:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23123400 Comparison Time: 30:13:03 (hh:mm:ss) Elapsed Time, 581679 HSPs Collected Number of families returned by RECON: 60175 Round Time: 32:31:12 (hh:mm:ss) Elapsed Time : 1019 families discovered. RepeatScout/RECON discovery complete: 2136 families found Classification Time: 01:33:28 (hh:mm:ss) Elapsed Time Program Time: 39:34:41 (hh:mm:ss) Elapsed Time