RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SJO1yA/RM_19239.ThuApr241101172025 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: 1745517676 Database = /dev/shm/rModeler.SJO1yA/GCA_048593235.1_ASM4859323v1 - Sequences = 7 - Bases = 3239981553 Storage Throughput = excellent ( 1938.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040016 bp ( 40029893 non ambiguous ) - Num Contigs Represented = 7 - Sequence extraction : 00:05:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:19 (hh:mm:ss) Elapsed Time Round Time: 00:20:16 (hh:mm:ss) Elapsed Time : 327 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:30 (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... 14796 repeats masked totaling 3341333 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039947 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 10033698 bp After Masking: 6420923 bp Masked: 36.01 % -- Input Database Coverage: 10039947 bp out of 3239981553 bp ( 0.31 % ) Sampling Time: 00:01:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:07 (hh:mm:ss) Elapsed Time, 17529 HSPs Collected Number of families returned by RECON: 1483 Round Time: 00:05:29 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52607 repeats masked totaling 12085001 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039989 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 30036115 bp After Masking: 17251475 bp Masked: 42.56 % -- Input Database Coverage: 40079936 bp out of 3239981553 bp ( 1.24 % ) Sampling Time: 00:05:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:37 (hh:mm:ss) Elapsed Time, 26785 HSPs Collected Number of families returned by RECON: 3192 Round Time: 00:18:45 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:13:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 168736 repeats masked totaling 39064220 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040100 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 90030258 bp After Masking: 48649790 bp Masked: 45.96 % -- Input Database Coverage: 130120036 bp out of 3239981553 bp ( 4.02 % ) Sampling Time: 00:17:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:14:51 (hh:mm:ss) Elapsed Time, 96446 HSPs Collected Number of families returned by RECON: 9999 Round Time: 01:33:37 (hh:mm:ss) Elapsed Time : 173 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:39:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 553136 repeats masked totaling 124284613 bp(s). - TE Masking time 00:02:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270040448 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 270004269 bp After Masking: 138633855 bp Masked: 48.65 % -- Input Database Coverage: 400160484 bp out of 3239981553 bp ( 12.35 % ) Sampling Time: 00:52:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22784625 Comparison Time: 08:54:35 (hh:mm:ss) Elapsed Time, 362914 HSPs Collected Number of families returned by RECON: 38637 Round Time: 10:00:45 (hh:mm:ss) Elapsed Time : 503 families discovered. RepeatScout/RECON discovery complete: 1101 families found Classification Time: 00:18:07 (hh:mm:ss) Elapsed Time Program Time: 12:36:59 (hh:mm:ss) Elapsed Time