RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.nrhuLp/RM_2236645.ThuApr241046472025 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: 1745516806 Database = /data/tmp/rModeler.nrhuLp/GCA_048593285.1_ASM4859328v1 - Sequences = 6 - Bases = 3043210118 Storage Throughput = excellent ( 1407.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034607 bp ( 40018885 non ambiguous ) - Num Contigs Represented = 6 - Sequence extraction : 00:06:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:01 (hh:mm:ss) Elapsed Time Round Time: 00:23:41 (hh:mm:ss) Elapsed Time : 318 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15362 repeats masked totaling 3342717 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039978 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 10024256 bp After Masking: 6534203 bp Masked: 34.82 % -- Input Database Coverage: 10039978 bp out of 3043210118 bp ( 0.33 % ) Sampling Time: 00:02:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:52 (hh:mm:ss) Elapsed Time, 20484 HSPs Collected Number of families returned by RECON: 1552 Round Time: 00:07:24 (hh:mm:ss) Elapsed Time : 33 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55481 repeats masked totaling 12283620 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034549 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 30034549 bp After Masking: 17255393 bp Masked: 42.55 % -- Input Database Coverage: 40074527 bp out of 3043210118 bp ( 1.32 % ) Sampling Time: 00:06:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:14:15 (hh:mm:ss) Elapsed Time, 26700 HSPs Collected Number of families returned by RECON: 3071 Round Time: 00:20:56 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:13:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 181754 repeats masked totaling 38314755 bp(s). - TE Masking time 00:01:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90080338 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 90012449 bp After Masking: 49785218 bp Masked: 44.69 % -- Input Database Coverage: 130154865 bp out of 3043210118 bp ( 4.28 % ) Sampling Time: 00:18:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:45:06 (hh:mm:ss) Elapsed Time, 74645 HSPs Collected Number of families returned by RECON: 10412 Round Time: 02:05:57 (hh:mm:ss) Elapsed Time : 164 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:36:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 591114 repeats masked totaling 122545850 bp(s). - TE Masking time 00:04:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270241240 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 270036604 bp After Masking: 142720642 bp Masked: 47.15 % -- Input Database Coverage: 400396105 bp out of 3043210118 bp ( 13.16 % ) Sampling Time: 00:53:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 14:43:07 (hh:mm:ss) Elapsed Time, 263752 HSPs Collected Number of families returned by RECON: 40191 Round Time: 15:56:48 (hh:mm:ss) Elapsed Time : 505 families discovered. RepeatScout/RECON discovery complete: 1094 families found Classification Time: 00:23:48 (hh:mm:ss) Elapsed Time Program Time: 19:18:34 (hh:mm:ss) Elapsed Time