RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.CT0b46/RM_1362496.MonApr211810362025 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: 1745284235 Database = /data/tmp/rModeler.CT0b46/GCA_041735815.1_T2T-goat2.0 - Sequences = 31 - Bases = 2863923675 Storage Throughput = good ( 829.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001033 bp ( 40001033 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:37 (hh:mm:ss) Elapsed Time Round Time: 00:32:32 (hh:mm:ss) Elapsed Time : 267 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14683 repeats masked totaling 3465693 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039619 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10039619 bp After Masking: 6360461 bp Masked: 36.65 % -- Input Database Coverage: 10039619 bp out of 2863923675 bp ( 0.35 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:35 (hh:mm:ss) Elapsed Time, 7594 HSPs Collected Number of families returned by RECON: 734 Round Time: 00:07:28 (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 : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48251 repeats masked totaling 11822813 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001336 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30001336 bp After Masking: 17691893 bp Masked: 41.03 % -- Input Database Coverage: 40040955 bp out of 2863923675 bp ( 1.40 % ) Sampling Time: 00:03:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:22:19 (hh:mm:ss) Elapsed Time, 19380 HSPs Collected Number of families returned by RECON: 1966 Round Time: 00:28:21 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153434 repeats masked totaling 38052084 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003031 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90003031 bp After Masking: 50837219 bp Masked: 43.52 % -- Input Database Coverage: 130043986 bp out of 2863923675 bp ( 4.54 % ) Sampling Time: 00:08:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 02:24:17 (hh:mm:ss) Elapsed Time, 74509 HSPs Collected Number of families returned by RECON: 6231 Round Time: 02:43:24 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 491281 repeats masked totaling 118522850 bp(s). - TE Masking time 00:06:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270005629 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 270005629 bp After Masking: 147467716 bp Masked: 45.38 % -- Input Database Coverage: 400049615 bp out of 2863923675 bp ( 13.97 % ) Sampling Time: 00:29:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 18:33:09 (hh:mm:ss) Elapsed Time, 159011 HSPs Collected Number of families returned by RECON: 27865 Round Time: 20:59:00 (hh:mm:ss) Elapsed Time : 349 families discovered. RepeatScout/RECON discovery complete: 859 families found Classification Time: 00:34:30 (hh:mm:ss) Elapsed Time Program Time: 25:25:15 (hh:mm:ss) Elapsed Time