RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.L1sHNM/RM_26377.SunJul211140222024 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: 1721587220 Database = /dev/shm/rModeler.L1sHNM/GCF_018296145.1_Otsh_v2.0 - Sequences = 7665 - Bases = 2294859190 - N50 = 75537397 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 89415124-95801903 | [ 5 ] 83028345-89415123 | [ 2 ] 76641567-83028345 | [ 3 ] 70254788-76641566 | [ 3 ] 63868010-70254788 | [ ] 57481231-63868009 | [ 2 ] 51094453-57481231 | [ 4 ] 44707674-51094452 | [ 6 ] 38320896-44707674 | [ 3 ] 31934117-38320895 | [ 1 ] 25547339-31934117 | [ 1 ] 19160560-25547338 | [ 2 ] 12773782-19160560 | [ 2 ] 6387003-12773781 | [ ] 225-6387003 |************************************************** [ 7631 ] Storage Throughput = excellent ( 1120.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028814 bp ( 40025114 non ambiguous ) - Num Contigs Represented = 258 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:29 (hh:mm:ss) Elapsed Time Round Time: 00:34:23 (hh:mm:ss) Elapsed Time : 839 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13066 repeats masked totaling 3531091 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019380 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 10017880 bp After Masking: 4011998 bp Masked: 59.95 % -- Input Database Coverage: 10019380 bp out of 2294859190 bp ( 0.44 % ) Sampling Time: 00:09:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36585 Comparison Time: 00:12:37 (hh:mm:ss) Elapsed Time, 4821 HSPs Collected Number of families returned by RECON: 1138 Round Time: 00:23:00 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40547 repeats masked totaling 10795168 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009426 bp Num Contigs Represented = 205 Non ambiguous bp: Initial: 30007226 bp After Masking: 12686281 bp Masked: 57.72 % -- Input Database Coverage: 40028806 bp out of 2294859190 bp ( 1.74 % ) Sampling Time: 00:22:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 342378 Comparison Time: 00:46:38 (hh:mm:ss) Elapsed Time, 36782 HSPs Collected Number of families returned by RECON: 3524 Round Time: 01:11:36 (hh:mm:ss) Elapsed Time : 106 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:04:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 129995 repeats masked totaling 33831158 bp(s). - TE Masking time 00:02:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038160 bp Num Contigs Represented = 529 Non ambiguous bp: Initial: 90027993 bp After Masking: 36782041 bp Masked: 59.14 % -- Input Database Coverage: 130066966 bp out of 2294859190 bp ( 5.67 % ) Sampling Time: 01:09:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3083886 Comparison Time: 03:37:17 (hh:mm:ss) Elapsed Time, 239827 HSPs Collected Number of families returned by RECON: 10789 Round Time: 05:00:06 (hh:mm:ss) Elapsed Time : 469 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:23:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 438025 repeats masked totaling 112579552 bp(s). - TE Masking time 00:09:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270063443 bp Num Contigs Represented = 1366 Non ambiguous bp: Initial: 270039341 bp After Masking: 97935576 bp Masked: 63.73 % -- Input Database Coverage: 400130409 bp out of 2294859190 bp ( 17.44 % ) Sampling Time: 03:41:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 27346710 Comparison Time: 30:17:15 (hh:mm:ss) Elapsed Time, 616379 HSPs Collected Number of families returned by RECON: 35494 Round Time: 35:21:18 (hh:mm:ss) Elapsed Time : 961 families discovered. RepeatScout/RECON discovery complete: 2380 families found Classification Time: 01:36:30 (hh:mm:ss) Elapsed Time Program Time: 44:06:54 (hh:mm:ss) Elapsed Time