RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.w3PT5p/RM_19079.WedOct161008042024 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: 1729098468 Database = /dev/shm/rModeler.w3PT5p/GCF_003003495.1_ASM300349v1 - Sequences = 1 - Bases = 2046572 Storage Throughput = fair ( 650.91 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 2046514 bp ( 2046514 non ambiguous ) - Num Contigs Represented = 1 - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:01:04 (hh:mm:ss) Elapsed Time Round Time: 00:12:43 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 361 repeats masked totaling 42217 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 2046514 bp Num Contigs Represented = 1 Non ambiguous bp: Initial: 2046514 bp After Masking: 1997735 bp Masked: 2.38 % -- Input Database Coverage: 2046514 bp out of 2046572 bp ( 100.00 % ) Sampling Time: 00:01:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1326 Comparison Time: 00:40:30 (hh:mm:ss) Elapsed Time, 1186 HSPs Collected Number of families returned by RECON: 228 Round Time: 00:46:20 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatScout/RECON discovery complete: 8 families found Classification Time: 00:01:58 (hh:mm:ss) Elapsed Time Program Time: 01:01:01 (hh:mm:ss) Elapsed Time