RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.YYvnOi/RM_3943678.WedJun260358452024 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: 1719399525 Database = /dev/shm/rModeler.YYvnOi/GCF_037176945.1_fLatCha1.pri - Sequences = 197 - Bases = 2947609019 - N50 = 264120050 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 403264244-432068277 | [ 1 ] 374460212-403264244 | [ 1 ] 345656179-374460211 | [ ] 316852147-345656179 | [ ] 288048115-316852147 | [ ] 259244082-288048114 | [ 2 ] 230440050-259244082 | [ ] 201636017-230440049 | [ ] 172831985-201636017 | [ 1 ] 144027953-172831985 | [ 3 ] 115223920-144027952 | [ ] 86419888-115223920 | [ 1 ] 57615855-86419887 | [ 2 ] 28811823-57615855 |*** [ 12 ] 7791-28811823 |************************************************** [ 174 ] Storage Throughput = good ( 890.50 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033682 bp ( 40033282 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:04:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:52 (hh:mm:ss) Elapsed Time Round Time: 00:30:50 (hh:mm:ss) Elapsed Time : 728 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22591 repeats masked totaling 5292861 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026868 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10026668 bp After Masking: 4578442 bp Masked: 54.34 % -- Input Database Coverage: 10026868 bp out of 2947609019 bp ( 0.34 % ) Sampling Time: 00:01:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:08 (hh:mm:ss) Elapsed Time, 10179 HSPs Collected Number of families returned by RECON: 1528 Round Time: 00:08:26 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68164 repeats masked totaling 16785493 bp(s). - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006734 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30006534 bp After Masking: 12705470 bp Masked: 57.66 % -- Input Database Coverage: 40033602 bp out of 2947609019 bp ( 1.36 % ) Sampling Time: 00:06:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:27:03 (hh:mm:ss) Elapsed Time, 50238 HSPs Collected Number of families returned by RECON: 4405 Round Time: 00:34:50 (hh:mm:ss) Elapsed Time : 135 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 220449 repeats masked totaling 52651256 bp(s). - TE Masking time 00:03:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037175 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 90036175 bp After Masking: 35607049 bp Masked: 60.45 % -- Input Database Coverage: 130070777 bp out of 2947609019 bp ( 4.41 % ) Sampling Time: 00:18:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:42:59 (hh:mm:ss) Elapsed Time, 239277 HSPs Collected Number of families returned by RECON: 12169 Round Time: 03:10:18 (hh:mm:ss) Elapsed Time : 496 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:30:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 725990 repeats masked totaling 171555132 bp(s). - TE Masking time 00:17:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270010535 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 270008135 bp After Masking: 93971981 bp Masked: 65.20 % -- Input Database Coverage: 400081312 bp out of 2947609019 bp ( 13.57 % ) Sampling Time: 01:03:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 18:22:31 (hh:mm:ss) Elapsed Time, 706412 HSPs Collected Number of families returned by RECON: 35035 Round Time: 20:13:05 (hh:mm:ss) Elapsed Time : 1290 families discovered. RepeatScout/RECON discovery complete: 2678 families found Classification Time: 01:37:35 (hh:mm:ss) Elapsed Time Program Time: 26:15:04 (hh:mm:ss) Elapsed Time