RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ARv7bB/RM_1949424.SatApr190622352025 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: 1745068952 Database = /dev/shm/rModeler.ARv7bB/GCF_028372415.1_mMacEug1.pri_v2 - Sequences = 272 - Bases = 3447464908 - N50 = 539575378 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 711411000-762225844 | [ 1 ] 660596156-711410999 | [ ] 609781312-660596155 | [ ] 558966468-609781311 | [ ] 508151625-558966468 | [ 1 ] 457336781-508151624 | [ 3 ] 406521937-457336780 | [ ] 355707093-406521936 | [ 1 ] 304892249-355707092 | [ ] 254077406-304892249 | [ ] 203262562-254077405 | [ ] 152447718-203262561 | [ 1 ] 101632874-152447717 | [ 1 ] 50818030-101632873 | [ ] 3187-50818030 |************************************************** [ 264 ] Storage Throughput = excellent ( 1796.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027114 bp ( 40020038 non ambiguous ) - Num Contigs Represented = 20 - Sequence extraction : 00:05:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:04 (hh:mm:ss) Elapsed Time Round Time: 00:16:59 (hh:mm:ss) Elapsed Time : 320 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20063 repeats masked totaling 3624988 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008885 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 10005446 bp After Masking: 6146020 bp Masked: 38.57 % -- Input Database Coverage: 10008885 bp out of 3447464908 bp ( 0.29 % ) Sampling Time: 00:01:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:30 (hh:mm:ss) Elapsed Time, 51909 HSPs Collected Number of families returned by RECON: 1254 Round Time: 00:06:45 (hh:mm:ss) Elapsed Time : 37 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:55 (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... 69330 repeats masked totaling 13314009 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018149 bp Num Contigs Represented = 15 Non ambiguous bp: Initial: 30014512 bp After Masking: 16259606 bp Masked: 45.83 % -- Input Database Coverage: 40027034 bp out of 3447464908 bp ( 1.16 % ) Sampling Time: 00:04:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:16:06 (hh:mm:ss) Elapsed Time, 30404 HSPs Collected Number of families returned by RECON: 2698 Round Time: 00:21:22 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 214667 repeats masked totaling 42262178 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90165372 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 90024097 bp After Masking: 46172521 bp Masked: 48.71 % -- Input Database Coverage: 130192406 bp out of 3447464908 bp ( 3.78 % ) Sampling Time: 00:15:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:36:40 (hh:mm:ss) Elapsed Time, 253653 HSPs Collected Number of families returned by RECON: 9311 Round Time: 01:54:21 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:34:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 686686 repeats masked totaling 134124890 bp(s). - TE Masking time 00:02:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270631654 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 270019526 bp After Masking: 130880827 bp Masked: 51.53 % -- Input Database Coverage: 400824060 bp out of 3447464908 bp ( 11.63 % ) Sampling Time: 00:45:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 09:07:57 (hh:mm:ss) Elapsed Time, 1544539 HSPs Collected Number of families returned by RECON: 34952 Round Time: 10:12:30 (hh:mm:ss) Elapsed Time : 497 families discovered. RepeatScout/RECON discovery complete: 1074 families found Classification Time: 00:19:04 (hh:mm:ss) Elapsed Time Program Time: 13:11:01 (hh:mm:ss) Elapsed Time