RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6c1SOg/RM_4558.TueAug130118282024 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: 1723537107 Database = /dev/shm/rModeler.6c1SOg/GCA_003971505.1_ASM397150v1 - Sequences = 8 - Bases = 28307147 Storage Throughput = good ( 980.21 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 28307066 bp ( 28307066 non ambiguous ) - Num Contigs Represented = 8 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:06 (hh:mm:ss) Elapsed Time Round Time: 00:11:15 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 749 repeats masked totaling 446394 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027370 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 10027370 bp After Masking: 9549538 bp Masked: 4.77 % -- Input Database Coverage: 10027370 bp out of 28307147 bp ( 35.42 % ) Sampling Time: 00:00:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:41 (hh:mm:ss) Elapsed Time, 1708 HSPs Collected Number of families returned by RECON: 636 Round Time: 00:06:10 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1119 repeats masked totaling 685858 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 18279677 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 18279677 bp After Masking: 17539709 bp Masked: 4.05 % -- Input Database Coverage: 28307047 bp out of 28307147 bp ( 100.00 % ) Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 106491 Comparison Time: 00:11:01 (hh:mm:ss) Elapsed Time, 4754 HSPs Collected Number of families returned by RECON: 1590 Round Time: 00:11:48 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatScout/RECON discovery complete: 63 families found Classification Time: 00:05:56 (hh:mm:ss) Elapsed Time Program Time: 00:35:09 (hh:mm:ss) Elapsed Time