RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.eTbNls/RM_863912.ThuFeb270133382025 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: 1740648815 Database = /dev/shm/rModeler.eTbNls/GCA_047948205.1_ASM4794820v1 - Sequences = 13 - Bases = 2217731716 Storage Throughput = excellent ( 1671.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001593 bp ( 40001393 non ambiguous ) - Num Contigs Represented = 13 - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:36 (hh:mm:ss) Elapsed Time Round Time: 00:13:29 (hh:mm:ss) Elapsed Time : 738 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (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... 12842 repeats masked totaling 3225764 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000179 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 10000179 bp After Masking: 6724660 bp Masked: 32.75 % -- Input Database Coverage: 10000179 bp out of 2217731716 bp ( 0.45 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:04 (hh:mm:ss) Elapsed Time, 10829 HSPs Collected Number of families returned by RECON: 1401 Round Time: 00:06:36 (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 : 00:01:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42392 repeats masked totaling 10437040 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001411 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 30001211 bp After Masking: 19253022 bp Masked: 35.83 % -- Input Database Coverage: 40001590 bp out of 2217731716 bp ( 1.80 % ) Sampling Time: 00:03:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:21:20 (hh:mm:ss) Elapsed Time, 50635 HSPs Collected Number of families returned by RECON: 4201 Round Time: 00:25:01 (hh:mm:ss) Elapsed Time : 105 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138283 repeats masked totaling 33961268 bp(s). - TE Masking time 00:02:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90005274 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 90004674 bp After Masking: 55179923 bp Masked: 38.69 % -- Input Database Coverage: 130006864 bp out of 2217731716 bp ( 5.86 % ) Sampling Time: 00:10:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 02:20:48 (hh:mm:ss) Elapsed Time, 276660 HSPs Collected Number of families returned by RECON: 11422 Round Time: 02:36:01 (hh:mm:ss) Elapsed Time : 465 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 480293 repeats masked totaling 121732752 bp(s). - TE Masking time 00:09:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270005327 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 270003348 bp After Masking: 145009800 bp Masked: 46.29 % -- Input Database Coverage: 400012191 bp out of 2217731716 bp ( 18.04 % ) Sampling Time: 00:32:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22777875 Comparison Time: 15:34:13 (hh:mm:ss) Elapsed Time, 810232 HSPs Collected Number of families returned by RECON: 29456 Round Time: 16:23:50 (hh:mm:ss) Elapsed Time : 1088 families discovered. RepeatScout/RECON discovery complete: 2414 families found Classification Time: 01:08:01 (hh:mm:ss) Elapsed Time Program Time: 20:52:58 (hh:mm:ss) Elapsed Time