RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.VVQfQJ/RM_26372.FriDec62346302024 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: 1733557589 Database = /scratch/tmp/rModeler.VVQfQJ/GCA_037176775.1_rAnoSag1.pat - Sequences = 41 - Bases = 1727284250 Storage Throughput = fair ( 654.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005547 bp ( 40004747 non ambiguous ) - Num Contigs Represented = 16 - Sequence extraction : 00:05:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:59 (hh:mm:ss) Elapsed Time Round Time: 00:29:33 (hh:mm:ss) Elapsed Time : 640 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21703 repeats masked totaling 4110621 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035789 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 10035789 bp After Masking: 5593027 bp Masked: 44.27 % -- Input Database Coverage: 10035789 bp out of 1727284250 bp ( 0.58 % ) Sampling Time: 00:02:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:14 (hh:mm:ss) Elapsed Time, 41829 HSPs Collected Number of families returned by RECON: 1156 Round Time: 00:08:50 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:48 (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... 67632 repeats masked totaling 12250447 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009678 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 30008878 bp After Masking: 16810951 bp Masked: 43.98 % -- Input Database Coverage: 40045467 bp out of 1727284250 bp ( 2.32 % ) Sampling Time: 00:06:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:26:21 (hh:mm:ss) Elapsed Time, 39949 HSPs Collected Number of families returned by RECON: 3627 Round Time: 00:34:31 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 217764 repeats masked totaling 39787369 bp(s). - TE Masking time 00:02:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036795 bp Num Contigs Represented = 15 Non ambiguous bp: Initial: 90034795 bp After Masking: 47284196 bp Masked: 47.48 % -- Input Database Coverage: 130082262 bp out of 1727284250 bp ( 7.53 % ) Sampling Time: 00:19:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:45:05 (hh:mm:ss) Elapsed Time, 176878 HSPs Collected Number of families returned by RECON: 10175 Round Time: 03:14:36 (hh:mm:ss) Elapsed Time : 393 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:33:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 718056 repeats masked totaling 130000452 bp(s). - TE Masking time 00:11:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032429 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 270028029 bp After Masking: 131184321 bp Masked: 51.42 % -- Input Database Coverage: 400114691 bp out of 1727284250 bp ( 23.16 % ) Sampling Time: 01:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 20:12:38 (hh:mm:ss) Elapsed Time, 421084 HSPs Collected Number of families returned by RECON: 33133 Round Time: 22:09:49 (hh:mm:ss) Elapsed Time : 858 families discovered. RepeatScout/RECON discovery complete: 2010 families found Classification Time: 01:05:00 (hh:mm:ss) Elapsed Time Program Time: 27:42:19 (hh:mm:ss) Elapsed Time