RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.F9uflb/RM_479550.SunApr201311342025 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: 1745179894 Database = /data/tmp/rModeler.F9uflb/GCA_023333525.2_rAspTig1.1.pri - Sequences = 186 - Bases = 1673115766 - N50 = 179774429 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 276850556-296624713 | [ 1 ] 257076399-276850555 | [ ] 237302243-257076399 | [ ] 217528086-237302242 | [ ] 197753929-217528085 | [ 1 ] 177979773-197753929 | [ 1 ] 158205616-177979772 | [ ] 138431459-158205615 | [ ] 118657303-138431459 | [ 1 ] 98883146-118657302 | [ 2 ] 79108989-98883145 | [ 3 ] 59334833-79108989 | [ 2 ] 39560676-59334832 | [ ] 19786519-39560675 |* [ 5 ] 12363-19786519 |************************************************** [ 170 ] Storage Throughput = good ( 863.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037131 bp ( 40036931 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:04:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:09 (hh:mm:ss) Elapsed Time Round Time: 00:33:59 (hh:mm:ss) Elapsed Time : 635 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:12 (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... 20264 repeats masked totaling 3307348 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000529 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10000429 bp After Masking: 6194600 bp Masked: 38.06 % -- Input Database Coverage: 10000529 bp out of 1673115766 bp ( 0.60 % ) Sampling Time: 00:02:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:12 (hh:mm:ss) Elapsed Time, 17330 HSPs Collected Number of families returned by RECON: 1408 Round Time: 00:10:00 (hh:mm:ss) Elapsed Time : 32 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62944 repeats masked totaling 10968866 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036599 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30036499 bp After Masking: 17651147 bp Masked: 41.23 % -- Input Database Coverage: 40037128 bp out of 1673115766 bp ( 2.39 % ) Sampling Time: 00:07:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:25:32 (hh:mm:ss) Elapsed Time, 46208 HSPs Collected Number of families returned by RECON: 4165 Round Time: 00:38:57 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 200065 repeats masked totaling 34290459 bp(s). - TE Masking time 00:02:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90033407 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 90033307 bp After Masking: 50994484 bp Masked: 43.36 % -- Input Database Coverage: 130070535 bp out of 1673115766 bp ( 7.77 % ) Sampling Time: 00:23:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 02:43:11 (hh:mm:ss) Elapsed Time, 188387 HSPs Collected Number of families returned by RECON: 12595 Round Time: 03:33:06 (hh:mm:ss) Elapsed Time : 402 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:28:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 662445 repeats masked totaling 114458909 bp(s). - TE Masking time 00:10:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270015462 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 270013250 bp After Masking: 143827173 bp Masked: 46.73 % -- Input Database Coverage: 400085997 bp out of 1673115766 bp ( 23.91 % ) Sampling Time: 01:07:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 18:25:27 (hh:mm:ss) Elapsed Time, 519429 HSPs Collected Number of families returned by RECON: 42154 Round Time: 21:39:55 (hh:mm:ss) Elapsed Time : 1075 families discovered. RepeatScout/RECON discovery complete: 2240 families found Classification Time: 01:08:50 (hh:mm:ss) Elapsed Time Program Time: 27:44:47 (hh:mm:ss) Elapsed Time