RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.DCbQwF/RM_2330464.WedNov132031062024 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: 1731558665 Database = /scratch/tmp/rModeler.DCbQwF/GCA_037176765.1_rAnoSag1.mat - Sequences = 29 - Bases = 1950830970 Storage Throughput = excellent ( 1444.32 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002086 bp ( 40001486 non ambiguous ) - Num Contigs Represented = 16 - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:35 (hh:mm:ss) Elapsed Time Round Time: 00:11:46 (hh:mm:ss) Elapsed Time : 664 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21781 repeats masked totaling 4255507 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000601 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 10000401 bp After Masking: 5213305 bp Masked: 47.87 % -- Input Database Coverage: 10000601 bp out of 1950830970 bp ( 0.51 % ) Sampling Time: 00:01:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:05 (hh:mm:ss) Elapsed Time, 8830 HSPs Collected Number of families returned by RECON: 1085 Round Time: 00:04:54 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67240 repeats masked totaling 12891413 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001405 bp Num Contigs Represented = 15 Non ambiguous bp: Initial: 30001005 bp After Masking: 16028463 bp Masked: 46.57 % -- Input Database Coverage: 40002006 bp out of 1950830970 bp ( 2.05 % ) Sampling Time: 00:03:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:11:20 (hh:mm:ss) Elapsed Time, 42360 HSPs Collected Number of families returned by RECON: 3423 Round Time: 00:15:25 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 215125 repeats masked totaling 41161915 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90005022 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 90002736 bp After Masking: 45240940 bp Masked: 49.73 % -- Input Database Coverage: 130007028 bp out of 1950830970 bp ( 6.66 % ) Sampling Time: 00:09:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:00:15 (hh:mm:ss) Elapsed Time, 181673 HSPs Collected Number of families returned by RECON: 10315 Round Time: 01:13:51 (hh:mm:ss) Elapsed Time : 385 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 703458 repeats masked totaling 132827305 bp(s). - TE Masking time 00:03:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270015087 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 270010156 bp After Masking: 125195120 bp Masked: 53.63 % -- Input Database Coverage: 400022115 bp out of 1950830970 bp ( 20.51 % ) Sampling Time: 00:29:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 06:15:41 (hh:mm:ss) Elapsed Time, 456336 HSPs Collected Number of families returned by RECON: 32538 Round Time: 07:08:18 (hh:mm:ss) Elapsed Time : 840 families discovered. RepeatScout/RECON discovery complete: 2013 families found Classification Time: 00:35:22 (hh:mm:ss) Elapsed Time Program Time: 09:29:36 (hh:mm:ss) Elapsed Time