RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.uNFEvu/RM_4052527.ThuApr101848362025 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: 1744336116 Database = /dev/shm/rModeler.uNFEvu/GCA_965140235.1_rCarCar1.hap1 - Sequences = 36 - Bases = 2217236305 Storage Throughput = excellent ( 1706.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023448 bp ( 40023448 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:53 (hh:mm:ss) Elapsed Time Round Time: 00:11:29 (hh:mm:ss) Elapsed Time : 507 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13744 repeats masked totaling 2996209 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022213 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10022213 bp After Masking: 6956741 bp Masked: 30.59 % -- Input Database Coverage: 10022213 bp out of 2217236305 bp ( 0.45 % ) Sampling Time: 00:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:49 (hh:mm:ss) Elapsed Time, 11958 HSPs Collected Number of families returned by RECON: 1601 Round Time: 00:03:46 (hh:mm:ss) Elapsed Time : 37 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45158 repeats masked totaling 9728324 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001155 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30001155 bp After Masking: 20130094 bp Masked: 32.90 % -- Input Database Coverage: 40023368 bp out of 2217236305 bp ( 1.81 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:12:37 (hh:mm:ss) Elapsed Time, 83886 HSPs Collected Number of families returned by RECON: 4994 Round Time: 00:15:21 (hh:mm:ss) Elapsed Time : 141 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149266 repeats masked totaling 33168624 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003833 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90003420 bp After Masking: 56213804 bp Masked: 37.54 % -- Input Database Coverage: 130027201 bp out of 2217236305 bp ( 5.86 % ) Sampling Time: 00:06:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 01:07:34 (hh:mm:ss) Elapsed Time, 413015 HSPs Collected Number of families returned by RECON: 13789 Round Time: 01:18:18 (hh:mm:ss) Elapsed Time : 447 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 515422 repeats masked totaling 114995743 bp(s). - TE Masking time 00:03:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270136168 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 270025457 bp After Masking: 153383356 bp Masked: 43.20 % -- Input Database Coverage: 400163369 bp out of 2217236305 bp ( 18.05 % ) Sampling Time: 00:20:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 07:16:36 (hh:mm:ss) Elapsed Time, 3125991 HSPs Collected Number of families returned by RECON: 43557 Round Time: 08:00:21 (hh:mm:ss) Elapsed Time : 1029 families discovered. RepeatScout/RECON discovery complete: 2161 families found Classification Time: 00:41:28 (hh:mm:ss) Elapsed Time Program Time: 10:30:43 (hh:mm:ss) Elapsed Time