RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.tlC1Lo/RM_1089586.MonApr211338182025 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: 1745267897 Database = /dev/shm/rModeler.tlC1Lo/GCA_040805955.1_T2T-sheep1.0 - Sequences = 28 - Bases = 2853626077 Storage Throughput = excellent ( 1810.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000953 bp ( 40000953 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:45 (hh:mm:ss) Elapsed Time Round Time: 00:12:48 (hh:mm:ss) Elapsed Time : 262 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (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... 14287 repeats masked totaling 3521139 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000185 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10000185 bp After Masking: 6366654 bp Masked: 36.33 % -- Input Database Coverage: 10000185 bp out of 2853626077 bp ( 0.35 % ) Sampling Time: 00:00:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:00 (hh:mm:ss) Elapsed Time, 15572 HSPs Collected Number of families returned by RECON: 755 Round Time: 00:03:35 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49478 repeats masked totaling 12171015 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000688 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30000688 bp After Masking: 17418341 bp Masked: 41.94 % -- Input Database Coverage: 40000873 bp out of 2853626077 bp ( 1.40 % ) Sampling Time: 00:01:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:12:41 (hh:mm:ss) Elapsed Time, 14805 HSPs Collected Number of families returned by RECON: 1857 Round Time: 00:14:34 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157018 repeats masked totaling 37778400 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031124 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 90031124 bp After Masking: 51344058 bp Masked: 42.97 % -- Input Database Coverage: 130031997 bp out of 2853626077 bp ( 4.56 % ) Sampling Time: 00:03:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:07:00 (hh:mm:ss) Elapsed Time, 75474 HSPs Collected Number of families returned by RECON: 6971 Round Time: 01:12:07 (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 : 00:03:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 506696 repeats masked totaling 119546801 bp(s). - TE Masking time 00:02:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270038280 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 270038280 bp After Masking: 147989002 bp Masked: 45.20 % -- Input Database Coverage: 400070277 bp out of 2853626077 bp ( 14.02 % ) Sampling Time: 00:11:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 08:05:33 (hh:mm:ss) Elapsed Time, 193661 HSPs Collected Number of families returned by RECON: 28257 Round Time: 08:24:02 (hh:mm:ss) Elapsed Time : 320 families discovered. RepeatScout/RECON discovery complete: 827 families found Classification Time: 00:17:30 (hh:mm:ss) Elapsed Time Program Time: 10:24:36 (hh:mm:ss) Elapsed Time