RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.tgCq1z/RM_1101802.TueApr150456392025 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: 1744718197 Database = /dev/shm/rModeler.tgCq1z/GCA_043728145.1_ASM4372814v1 - Sequences = 126 - Bases = 2232422560 - N50 = 187817605 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 206120186-220842049 | [ 2 ] 191398323-206120185 | [ 2 ] 176676460-191398322 | [ 2 ] 161954597-176676459 | [ 1 ] 147232734-161954596 | [ ] 132510871-147232733 | [ ] 117789008-132510870 | [ 1 ] 103067146-117789008 | [ 1 ] 88345283-103067145 | [ 2 ] 73623420-88345282 | [ 2 ] 58901557-73623419 | [ ] 44179694-58901556 |* [ 3 ] 29457831-44179693 | [ 1 ] 14735968-29457830 | [ ] 14106-14735968 |************************************************* [ 109 ] Storage Throughput = excellent ( 1862.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003571 bp ( 40001851 non ambiguous ) - Num Contigs Represented = 39 - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:25 (hh:mm:ss) Elapsed Time Round Time: 00:14:08 (hh:mm:ss) Elapsed Time : 206 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9433 repeats masked totaling 2422381 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036558 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10035318 bp After Masking: 7458325 bp Masked: 25.68 % -- Input Database Coverage: 10036558 bp out of 2232422560 bp ( 0.45 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 10636 HSPs Collected Number of families returned by RECON: 723 Round Time: 00:03:53 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28981 repeats masked totaling 8144253 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007013 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30006533 bp After Masking: 21415872 bp Masked: 28.63 % -- Input Database Coverage: 40043571 bp out of 2232422560 bp ( 1.79 % ) Sampling Time: 00:02:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:13:08 (hh:mm:ss) Elapsed Time, 29447 HSPs Collected Number of families returned by RECON: 2526 Round Time: 00:16:47 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 97325 repeats masked totaling 27036190 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035165 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 90029745 bp After Masking: 61899015 bp Masked: 31.25 % -- Input Database Coverage: 130078736 bp out of 2232422560 bp ( 5.83 % ) Sampling Time: 00:06:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 01:12:40 (hh:mm:ss) Elapsed Time, 75473 HSPs Collected Number of families returned by RECON: 8715 Round Time: 01:20:05 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 332745 repeats masked totaling 89623364 bp(s). - TE Masking time 00:02:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270060130 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 270037526 bp After Masking: 177222736 bp Masked: 34.37 % -- Input Database Coverage: 400138866 bp out of 2232422560 bp ( 17.92 % ) Sampling Time: 00:18:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 08:09:35 (hh:mm:ss) Elapsed Time, 198339 HSPs Collected Number of families returned by RECON: 35491 Round Time: 08:42:20 (hh:mm:ss) Elapsed Time : 348 families discovered. RepeatScout/RECON discovery complete: 805 families found Classification Time: 00:20:18 (hh:mm:ss) Elapsed Time Program Time: 10:57:31 (hh:mm:ss) Elapsed Time