RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.OD4emT/RM_29290.WedNov291344402023 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: 1701294279 Database = /dev/shm/rModeler.OD4emT/GCA_028858725.1_bColStr4.hap1 - Sequences = 189 - Bases = 1123441015 - N50 = 97552025 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 192816910-206588619 | [ 1 ] 179045201-192816909 | [ ] 165273493-179045201 | [ ] 151501784-165273492 | [ ] 137730076-151501784 | [ ] 123958367-137730075 | [ ] 110186658-123958366 | [ 1 ] 96414950-110186658 | [ 2 ] 82643241-96414949 | [ ] 68871533-82643241 | [ ] 55099824-68871532 | [ 1 ] 41328115-55099823 | [ 3 ] 27556407-41328115 |* [ 5 ] 13784698-27556406 |* [ 5 ] 12990-13784698 |************************************************** [ 171 ] Storage Throughput = excellent ( 1133.51 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40151263 bp ( 40003228 non ambiguous ) - Num Contigs Represented = 59 - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:38 (hh:mm:ss) Elapsed Time Round Time: 00:28:09 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3890 repeats masked totaling 1187607 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000984 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10000984 bp After Masking: 8471360 bp Masked: 15.29 % -- Input Database Coverage: 10000984 bp out of 1123441015 bp ( 0.89 % ) Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:59 (hh:mm:ss) Elapsed Time, 321 HSPs Collected Number of families returned by RECON: 166 Round Time: 00:07:02 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11299 repeats masked totaling 3766341 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30150272 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30002237 bp After Masking: 25211153 bp Masked: 15.97 % -- Input Database Coverage: 40151256 bp out of 1123441015 bp ( 3.57 % ) Sampling Time: 00:03:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:33:48 (hh:mm:ss) Elapsed Time, 4165 HSPs Collected Number of families returned by RECON: 1251 Round Time: 00:37:24 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35203 repeats masked totaling 11183130 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90237511 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 90013785 bp After Masking: 76077577 bp Masked: 15.48 % -- Input Database Coverage: 130388767 bp out of 1123441015 bp ( 11.61 % ) Sampling Time: 00:10:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 04:08:44 (hh:mm:ss) Elapsed Time, 46691 HSPs Collected Number of families returned by RECON: 8337 Round Time: 04:22:26 (hh:mm:ss) Elapsed Time : 91 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 116098 repeats masked totaling 36548507 bp(s). - TE Masking time 00:04:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271415652 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 270004190 bp After Masking: 225829207 bp Masked: 16.36 % -- Input Database Coverage: 401804419 bp out of 1123441015 bp ( 35.77 % ) Sampling Time: 00:30:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23157415 Comparison Time: 34:05:10 (hh:mm:ss) Elapsed Time, 172170 HSPs Collected Number of families returned by RECON: 56432 Round Time: 35:21:50 (hh:mm:ss) Elapsed Time : 226 families discovered. RepeatScout/RECON discovery complete: 439 families found Classification Time: 00:41:38 (hh:mm:ss) Elapsed Time Program Time: 41:38:29 (hh:mm:ss) Elapsed Time