RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QfBWcg/RM_805.SatJul130721482024 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: 1720880507 Database = /dev/shm/rModeler.QfBWcg/GCF_003368295.1_ASM336829v1 - Sequences = 6216 - Bases = 1820635050 - N50 = 23179244 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 34706147-37185075 | [ 5 ] 32227219-34706146 | [ 2 ] 29748291-32227218 | [ 5 ] 27269363-29748290 | [ 8 ] 24790436-27269363 | [ 6 ] 22311508-24790435 | [ 6 ] 19832580-22311507 | [ 7 ] 17353652-19832579 | [ 5 ] 14874724-17353651 | [ 3 ] 12395797-14874724 | [ 1 ] 9916869-12395796 | [ 2 ] 7437941-9916868 | [ ] 4959013-7437940 | [ 2 ] 2480085-4959012 | [ 8 ] 1158-2480085 |************************************************** [ 6156 ] Storage Throughput = excellent ( 1031.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021787 bp ( 40017287 non ambiguous ) - Num Contigs Represented = 397 - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:52 (hh:mm:ss) Elapsed Time Round Time: 00:29:27 (hh:mm:ss) Elapsed Time : 792 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11517 repeats masked totaling 2758765 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002957 bp Num Contigs Represented = 155 Non ambiguous bp: Initial: 10002157 bp After Masking: 6920743 bp Masked: 30.81 % -- Input Database Coverage: 10002957 bp out of 1820635050 bp ( 0.55 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35511 Comparison Time: 00:07:02 (hh:mm:ss) Elapsed Time, 6448 HSPs Collected Number of families returned by RECON: 1496 Round Time: 00:08:28 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33824 repeats masked totaling 7961006 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018797 bp Num Contigs Represented = 304 Non ambiguous bp: Initial: 30015097 bp After Masking: 21073311 bp Masked: 29.79 % -- Input Database Coverage: 40021754 bp out of 1820635050 bp ( 2.20 % ) Sampling Time: 00:03:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 318801 Comparison Time: 00:38:23 (hh:mm:ss) Elapsed Time, 51613 HSPs Collected Number of families returned by RECON: 5798 Round Time: 00:43:46 (hh:mm:ss) Elapsed Time : 122 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112320 repeats masked totaling 25283138 bp(s). - TE Masking time 00:03:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013242 bp Num Contigs Represented = 747 Non ambiguous bp: Initial: 90000422 bp After Masking: 61838098 bp Masked: 31.29 % -- Input Database Coverage: 130034996 bp out of 1820635050 bp ( 7.14 % ) Sampling Time: 00:10:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2845305 Comparison Time: 04:27:37 (hh:mm:ss) Elapsed Time, 325266 HSPs Collected Number of families returned by RECON: 18489 Round Time: 04:56:02 (hh:mm:ss) Elapsed Time : 602 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 411218 repeats masked totaling 91095131 bp(s). - TE Masking time 00:21:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046452 bp Num Contigs Represented = 1831 Non ambiguous bp: Initial: 270012218 bp After Masking: 170076239 bp Masked: 37.01 % -- Input Database Coverage: 400081448 bp out of 1820635050 bp ( 21.97 % ) Sampling Time: 00:42:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25657866 Comparison Time: 32:29:19 (hh:mm:ss) Elapsed Time, 1007738 HSPs Collected Number of families returned by RECON: 60243 Round Time: 35:12:37 (hh:mm:ss) Elapsed Time : 1344 families discovered. RepeatScout/RECON discovery complete: 2867 families found Classification Time: 02:42:01 (hh:mm:ss) Elapsed Time Program Time: 44:12:21 (hh:mm:ss) Elapsed Time