RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KQJdwf/RM_272037.SatJul191903042025 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: 1752976982 Database = /dev/shm/rModeler.KQJdwf/GCA_048593325.1_ASM4859332v1 - Sequences = 6 - Bases = 3116321655 Storage Throughput = excellent ( 1153.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40319920 bp ( 40020494 non ambiguous ) - Num Contigs Represented = 6 - Sequence extraction : 00:12:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:02 (hh:mm:ss) Elapsed Time Round Time: 00:44:42 (hh:mm:ss) Elapsed Time : 302 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:03:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16492 repeats masked totaling 3223379 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10079920 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 10019382 bp After Masking: 6585065 bp Masked: 34.28 % -- Input Database Coverage: 10079920 bp out of 3116321655 bp ( 0.32 % ) Sampling Time: 00:03:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:32 (hh:mm:ss) Elapsed Time, 10940 HSPs Collected Number of families returned by RECON: 1417 Round Time: 00:09:59 (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 : 00:09:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55627 repeats masked totaling 11340787 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30239920 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 30001032 bp After Masking: 18042430 bp Masked: 39.86 % -- Input Database Coverage: 40319840 bp out of 3116321655 bp ( 1.29 % ) Sampling Time: 00:11:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:29:14 (hh:mm:ss) Elapsed Time, 31391 HSPs Collected Number of families returned by RECON: 3893 Round Time: 00:41:54 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:27:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 192862 repeats masked totaling 38495766 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90724545 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 90024010 bp After Masking: 49729187 bp Masked: 44.76 % -- Input Database Coverage: 131044385 bp out of 3116321655 bp ( 4.21 % ) Sampling Time: 00:34:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 03:17:59 (hh:mm:ss) Elapsed Time, 91767 HSPs Collected Number of families returned by RECON: 9954 Round Time: 03:57:25 (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 : 01:23:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 610701 repeats masked totaling 122076059 bp(s). - TE Masking time 00:09:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272036159 bp Num Contigs Represented = 6 Non ambiguous bp: Initial: 270008897 bp After Masking: 142804969 bp Masked: 47.11 % -- Input Database Coverage: 403080544 bp out of 3116321655 bp ( 12.93 % ) Sampling Time: 01:46:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23123400 Comparison Time: 25:41:40 (hh:mm:ss) Elapsed Time, 244447 HSPs Collected Number of families returned by RECON: 39706 Round Time: 28:10:10 (hh:mm:ss) Elapsed Time : 468 families discovered. RepeatScout/RECON discovery complete: 1062 families found Classification Time: 00:38:07 (hh:mm:ss) Elapsed Time Program Time: 34:22:17 (hh:mm:ss) Elapsed Time