RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QSivfZ/RM_28146.TueJul231853272024 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: 1721785999 Database = /dev/shm/rModeler.QSivfZ/GCF_018398535.1_NCSU_Asbu1 - Sequences = 7421 - Bases = 854588855 - N50 = 1424915 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 6643883-7118375 | [ 3 ] 6169391-6643882 | [ ] 5694900-6169391 | [ 2 ] 5220408-5694899 | [ 4 ] 4745916-5220407 | [ 1 ] 4271425-4745916 | [ 4 ] 3796933-4271424 | [ 7 ] 3322441-3796932 | [ 9 ] 2847950-3322441 | [ 16 ] 2373458-2847949 | [ 27 ] 1898966-2373457 | [ 41 ] 1424475-1898966 | [ 50 ] 949983-1424474 | [ 80 ] 475491-949982 |* [ 203 ] 1000-475491 |************************************************** [ 6974 ] Storage Throughput = excellent ( 1038.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 45050224 bp ( 40009551 non ambiguous ) - Num Contigs Represented = 842 - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:12 (hh:mm:ss) Elapsed Time Round Time: 00:46:34 (hh:mm:ss) Elapsed Time : 547 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (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... 9062 repeats masked totaling 1565509 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11063057 bp Num Contigs Represented = 273 Non ambiguous bp: Initial: 10010935 bp After Masking: 8375703 bp Masked: 16.33 % -- Input Database Coverage: 11063057 bp out of 854588855 bp ( 1.29 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 55611 Comparison Time: 01:31:02 (hh:mm:ss) Elapsed Time, 7071 HSPs Collected Number of families returned by RECON: 1226 Round Time: 01:35:10 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30571 repeats masked totaling 5258237 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 34027149 bp Num Contigs Represented = 694 Non ambiguous bp: Initial: 30038598 bp After Masking: 24532813 bp Masked: 18.33 % -- Input Database Coverage: 45090206 bp out of 854588855 bp ( 5.28 % ) Sampling Time: 00:02:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 572985 Comparison Time: 03:48:57 (hh:mm:ss) Elapsed Time, 54277 HSPs Collected Number of families returned by RECON: 5010 Round Time: 03:57:25 (hh:mm:ss) Elapsed Time : 112 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104213 repeats masked totaling 17917892 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 101547045 bp Num Contigs Represented = 1555 Non ambiguous bp: Initial: 90010687 bp After Masking: 71347557 bp Masked: 20.73 % -- Input Database Coverage: 146637251 bp out of 854588855 bp ( 17.16 % ) Sampling Time: 00:05:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 5240703 Comparison Time: 13:25:43 (hh:mm:ss) Elapsed Time, 204175 HSPs Collected Number of families returned by RECON: 16754 Round Time: 13:57:22 (hh:mm:ss) Elapsed Time : 382 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 364049 repeats masked totaling 64281985 bp(s). - TE Masking time 00:10:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 301857586 bp Num Contigs Represented = 3389 Non ambiguous bp: Initial: 270006185 bp After Masking: 203535688 bp Masked: 24.62 % -- Input Database Coverage: 448494837 bp out of 854588855 bp ( 52.48 % ) Sampling Time: 00:20:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 46392528 Comparison Time: 63:14:14 (hh:mm:ss) Elapsed Time, 655670 HSPs Collected Number of families returned by RECON: 65531 Round Time: 65:39:33 (hh:mm:ss) Elapsed Time : 1026 families discovered. RepeatScout/RECON discovery complete: 2084 families found Classification Time: 01:25:26 (hh:mm:ss) Elapsed Time Program Time: 87:21:30 (hh:mm:ss) Elapsed Time