RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.1KNOil/RM_3664104.WedNov132218312024 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: 1731565111 Database = /scratch/tmp/rModeler.1KNOil/GCA_963993115.1_fAbrBra2.1 - Sequences = 208 - Bases = 1108218292 - N50 = 44545901 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 74607774-79936830 | [ 1 ] 69278719-74607774 | [ ] 63949664-69278719 | [ 1 ] 58620608-63949663 | [ 2 ] 53291553-58620608 | [ ] 47962498-53291553 | [ 1 ] 42633442-47962497 |* [ 6 ] 37304387-42633442 |* [ 5 ] 31975332-37304387 |* [ 6 ] 26646276-31975331 | [ 3 ] 21317221-26646276 | [ ] 15988166-21317221 | [ ] 10659110-15988165 | [ ] 5330055-10659110 | [ ] 1000-5330055 |************************************************** [ 183 ] Storage Throughput = excellent ( 1152.61 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036032 bp ( 40031555 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:19 (hh:mm:ss) Elapsed Time Round Time: 00:13:17 (hh:mm:ss) Elapsed Time : 1311 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 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16269 repeats masked totaling 3369522 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001311 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000711 bp After Masking: 6087340 bp Masked: 39.13 % -- Input Database Coverage: 10001311 bp out of 1108218292 bp ( 0.90 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 9100 HSPs Collected Number of families returned by RECON: 1871 Round Time: 00:04:12 (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 : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49095 repeats masked totaling 10582022 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034641 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30030764 bp After Masking: 18006781 bp Masked: 40.04 % -- Input Database Coverage: 40035952 bp out of 1108218292 bp ( 3.61 % ) Sampling Time: 00:02:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:13:59 (hh:mm:ss) Elapsed Time, 74728 HSPs Collected Number of families returned by RECON: 6314 Round Time: 00:17:45 (hh:mm:ss) Elapsed Time : 146 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 159523 repeats masked totaling 32812038 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011439 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 90000355 bp After Masking: 52394341 bp Masked: 41.78 % -- Input Database Coverage: 130047391 bp out of 1108218292 bp ( 11.73 % ) Sampling Time: 00:08:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 01:15:58 (hh:mm:ss) Elapsed Time, 525551 HSPs Collected Number of families returned by RECON: 17206 Round Time: 01:33:20 (hh:mm:ss) Elapsed Time : 764 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 571191 repeats masked totaling 119335381 bp(s). - TE Masking time 00:09:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046159 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 270011512 bp After Masking: 136446959 bp Masked: 49.47 % -- Input Database Coverage: 400093550 bp out of 1108218292 bp ( 36.10 % ) Sampling Time: 00:29:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 09:02:34 (hh:mm:ss) Elapsed Time, 1558977 HSPs Collected Number of families returned by RECON: 46621 Round Time: 10:14:31 (hh:mm:ss) Elapsed Time : 1907 families discovered. RepeatScout/RECON discovery complete: 4140 families found Classification Time: 01:27:04 (hh:mm:ss) Elapsed Time Program Time: 13:50:09 (hh:mm:ss) Elapsed Time