RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.qi9mY8/RM_2233056.ThuApr241046452025 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: 1745516805 Database = /data/tmp/rModeler.qi9mY8/GCA_048771995.1_bTaeGut7.mat - Sequences = 42 - Bases = 1141165377 Storage Throughput = excellent ( 1414.91 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001636 bp ( 40001636 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:12 (hh:mm:ss) Elapsed Time Round Time: 00:23:50 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2745 repeats masked totaling 1039971 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001856 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10001856 bp After Masking: 8616087 bp Masked: 13.86 % -- Input Database Coverage: 10001856 bp out of 1141165377 bp ( 0.88 % ) Sampling Time: 00:00:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:43 (hh:mm:ss) Elapsed Time, 573 HSPs Collected Number of families returned by RECON: 291 Round Time: 00:04:18 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8504 repeats masked totaling 2807312 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039700 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30039700 bp After Masking: 25724107 bp Masked: 14.37 % -- Input Database Coverage: 40041556 bp out of 1141165377 bp ( 3.51 % ) Sampling Time: 00:03:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:17:29 (hh:mm:ss) Elapsed Time, 11568 HSPs Collected Number of families returned by RECON: 1577 Round Time: 00:20:40 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25857 repeats masked totaling 7880227 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90049867 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 90031517 bp After Masking: 77657932 bp Masked: 13.74 % -- Input Database Coverage: 130091423 bp out of 1141165377 bp ( 11.40 % ) Sampling Time: 00:06:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:14:57 (hh:mm:ss) Elapsed Time, 102863 HSPs Collected Number of families returned by RECON: 10000 Round Time: 02:24:12 (hh:mm:ss) Elapsed Time : 104 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 90529 repeats masked totaling 29194957 bp(s). - TE Masking time 00:03:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270068428 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 270001464 bp After Masking: 228787095 bp Masked: 15.26 % -- Input Database Coverage: 400159851 bp out of 1141165377 bp ( 35.07 % ) Sampling Time: 00:20:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 19:21:44 (hh:mm:ss) Elapsed Time, 905608 HSPs Collected Number of families returned by RECON: 64413 Round Time: 20:08:19 (hh:mm:ss) Elapsed Time : 291 families discovered. RepeatScout/RECON discovery complete: 564 families found Classification Time: 00:38:05 (hh:mm:ss) Elapsed Time Program Time: 23:59:24 (hh:mm:ss) Elapsed Time