RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.TkixOR/RM_1329786.WedDec181111382024 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: 1734549098 Database = /dev/shm/rModeler.TkixOR/GCA_040206675.1_aAscTru1.hap2 - Sequences = 2779 - Bases = 3660446095 - N50 = 458978005 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 490012822-525013076 | [ 2 ] 455012569-490012822 | [ 1 ] 420012316-455012569 | [ ] 385012062-420012315 | [ 1 ] 350011809-385012062 | [ ] 315011556-350011809 | [ ] 280011302-315011555 | [ 1 ] 245011049-280011302 | [ ] 210010796-245011049 | [ ] 175010542-210010795 | [ ] 140010289-175010542 | [ ] 105010036-140010289 | [ 3 ] 70009782-105010035 | [ 1 ] 35009529-70009782 | [ 11 ] 9276-35009529 |************************************************** [ 2759 ] Storage Throughput = fair ( 490.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40052719 bp ( 40038458 non ambiguous ) - Num Contigs Represented = 139 - Sequence extraction : 00:12:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:42:24 (hh:mm:ss) Elapsed Time Round Time: 01:53:25 (hh:mm:ss) Elapsed Time : 1065 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16104 repeats masked totaling 4791739 bp(s). - TE Masking time 00:01:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006841 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 10003641 bp After Masking: 3586966 bp Masked: 64.14 % -- Input Database Coverage: 10006841 bp out of 3660446095 bp ( 0.27 % ) Sampling Time: 00:13:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:09:58 (hh:mm:ss) Elapsed Time, 7375 HSPs Collected Number of families returned by RECON: 1195 Round Time: 00:24:28 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:16:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:51:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49129 repeats masked totaling 14134977 bp(s). - TE Masking time 00:04:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30045798 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 30034737 bp After Masking: 11010913 bp Masked: 63.34 % -- Input Database Coverage: 40052639 bp out of 3660446095 bp ( 1.09 % ) Sampling Time: 01:12:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:47:29 (hh:mm:ss) Elapsed Time, 48018 HSPs Collected Number of families returned by RECON: 4163 Round Time: 02:02:58 (hh:mm:ss) Elapsed Time : 101 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 01:13:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:13:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157485 repeats masked totaling 43472334 bp(s). - TE Masking time 00:14:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90079421 bp Num Contigs Represented = 270 Non ambiguous bp: Initial: 90045577 bp After Masking: 31525930 bp Masked: 64.99 % -- Input Database Coverage: 130132060 bp out of 3660446095 bp ( 3.56 % ) Sampling Time: 04:42:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 04:58:51 (hh:mm:ss) Elapsed Time, 259557 HSPs Collected Number of families returned by RECON: 11435 Round Time: 10:09:03 (hh:mm:ss) Elapsed Time : 532 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:51:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 10:45:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 540606 repeats masked totaling 145673025 bp(s). - TE Masking time 01:01:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270127186 bp Num Contigs Represented = 651 Non ambiguous bp: Initial: 270036414 bp After Masking: 80993756 bp Masked: 70.01 % -- Input Database Coverage: 400259246 bp out of 3660446095 bp ( 10.93 % ) Sampling Time: 13:40:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23450976 Comparison Time: 38:24:33 (hh:mm:ss) Elapsed Time, 842576 HSPs Collected Number of families returned by RECON: 28168 Round Time: 54:35:44 (hh:mm:ss) Elapsed Time : 1477 families discovered. RepeatScout/RECON discovery complete: 3190 families found Classification Time: 06:25:52 (hh:mm:ss) Elapsed Time Program Time: 75:31:30 (hh:mm:ss) Elapsed Time