RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2yKGtQ/RM_24193.ThuJun270656162024 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: 1719496574 Database = /dev/shm/rModeler.2yKGtQ/GCF_035149785.1_rCanAsp1.hap2 - Sequences = 149 - Bases = 1530810380 - N50 = 265922563 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 321060903-343993754 | [ 1 ] 298128053-321060903 | [ ] 275195203-298128053 | [ ] 252262352-275195202 | [ 1 ] 229329502-252262352 | [ ] 206396652-229329502 | [ 1 ] 183463802-206396652 | [ ] 160530951-183463801 | [ ] 137598101-160530951 | [ ] 114665251-137598101 | [ 2 ] 91732401-114665251 | [ 1 ] 68799550-91732400 | [ 2 ] 45866700-68799550 | [ ] 22933850-45866700 |* [ 5 ] 1000-22933850 |************************************************* [ 136 ] Storage Throughput = excellent ( 1097.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026535 bp ( 40025935 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:04:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:17 (hh:mm:ss) Elapsed Time Round Time: 00:33:04 (hh:mm:ss) Elapsed Time : 336 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9285 repeats masked totaling 2989572 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000415 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10000415 bp After Masking: 6838178 bp Masked: 31.62 % -- Input Database Coverage: 10000415 bp out of 1530810380 bp ( 0.65 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:12 (hh:mm:ss) Elapsed Time, 9908 HSPs Collected Number of families returned by RECON: 1199 Round Time: 00:07:50 (hh:mm:ss) Elapsed Time : 27 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31923 repeats masked totaling 9339601 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026118 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30025518 bp After Masking: 20336403 bp Masked: 32.27 % -- Input Database Coverage: 40026533 bp out of 1530810380 bp ( 2.61 % ) Sampling Time: 00:04:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:27:56 (hh:mm:ss) Elapsed Time, 33959 HSPs Collected Number of families returned by RECON: 3801 Round Time: 00:33:39 (hh:mm:ss) Elapsed Time : 89 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109798 repeats masked totaling 30120757 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90003158 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90001758 bp After Masking: 58585984 bp Masked: 34.91 % -- Input Database Coverage: 130029691 bp out of 1530810380 bp ( 8.49 % ) Sampling Time: 00:13:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 03:11:27 (hh:mm:ss) Elapsed Time, 157354 HSPs Collected Number of families returned by RECON: 12188 Round Time: 03:33:21 (hh:mm:ss) Elapsed Time : 318 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:26:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 377436 repeats masked totaling 98361836 bp(s). - TE Masking time 00:08:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270018912 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 270015112 bp After Masking: 167409152 bp Masked: 38.00 % -- Input Database Coverage: 400048603 bp out of 1530810380 bp ( 26.13 % ) Sampling Time: 00:43:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22825146 Comparison Time: 24:53:36 (hh:mm:ss) Elapsed Time, 551714 HSPs Collected Number of families returned by RECON: 45612 Round Time: 26:39:47 (hh:mm:ss) Elapsed Time : 711 families discovered. RepeatScout/RECON discovery complete: 1481 families found Classification Time: 01:02:32 (hh:mm:ss) Elapsed Time Program Time: 32:30:13 (hh:mm:ss) Elapsed Time