RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.aobGTX/RM_301968.ThuApr241314452025 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: 1745525685 Database = /dev/shm/rModeler.aobGTX/GCA_048565385.1_mSaiBol1.pri - Sequences = 63 - Bases = 2747476440 Storage Throughput = excellent ( 1925.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036193 bp ( 40036193 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:50 (hh:mm:ss) Elapsed Time Round Time: 00:12:14 (hh:mm:ss) Elapsed Time : 227 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13648 repeats masked totaling 2958921 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000533 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000533 bp After Masking: 6668423 bp Masked: 33.32 % -- Input Database Coverage: 10000533 bp out of 2747476440 bp ( 0.36 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:43 (hh:mm:ss) Elapsed Time, 6118 HSPs Collected Number of families returned by RECON: 855 Round Time: 00:03:36 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44464 repeats masked totaling 9208341 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035657 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30035657 bp After Masking: 19921554 bp Masked: 33.67 % -- Input Database Coverage: 40036190 bp out of 2747476440 bp ( 1.46 % ) Sampling Time: 00:02:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:56 (hh:mm:ss) Elapsed Time, 61156 HSPs Collected Number of families returned by RECON: 2260 Round Time: 00:15:26 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 145403 repeats masked totaling 30900660 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039635 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90039235 bp After Masking: 56324813 bp Masked: 37.44 % -- Input Database Coverage: 130075825 bp out of 2747476440 bp ( 4.73 % ) Sampling Time: 00:06:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:12:08 (hh:mm:ss) Elapsed Time, 111216 HSPs Collected Number of families returned by RECON: 7638 Round Time: 01:20:14 (hh:mm:ss) Elapsed Time : 180 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 469665 repeats masked totaling 98933680 bp(s). - TE Masking time 00:02:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270010792 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 270010092 bp After Masking: 163036186 bp Masked: 39.62 % -- Input Database Coverage: 400086617 bp out of 2747476440 bp ( 14.56 % ) Sampling Time: 00:19:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 08:39:46 (hh:mm:ss) Elapsed Time, 1680427 HSPs Collected Number of families returned by RECON: 31570 Round Time: 09:07:30 (hh:mm:ss) Elapsed Time : 383 families discovered. RepeatScout/RECON discovery complete: 884 families found Classification Time: 00:17:45 (hh:mm:ss) Elapsed Time Program Time: 11:16:45 (hh:mm:ss) Elapsed Time