RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.IMW1e0/RM_1094935.WedNov130636312024 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: 1731508589 Database = /scratch/tmp/rModeler.IMW1e0/GCF_009819655.1_bSylAtr1.pri - Sequences = 190 - Bases = 1066804524 - N50 = 88576696 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 142981509-153194430 | [ 1 ] 132768589-142981509 | [ ] 122555669-132768589 | [ ] 112342749-122555669 | [ 2 ] 102129829-112342749 | [ ] 91916909-102129829 | [ ] 81703989-91916909 | [ 1 ] 71491068-81703988 | [ 2 ] 61278148-71491068 | [ 1 ] 51065228-61278148 | [ ] 40852308-51065228 | [ ] 30639388-40852308 | [ 3 ] 20426468-30639388 |* [ 5 ] 10213548-20426468 |** [ 7 ] 628-10213548 |************************************************** [ 168 ] Storage Throughput = excellent ( 1538.76 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40314500 bp ( 40005363 non ambiguous ) - Num Contigs Represented = 49 - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:10 (hh:mm:ss) Elapsed Time Round Time: 00:09:39 (hh:mm:ss) Elapsed Time : 115 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2319 repeats masked totaling 556165 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10124832 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10013544 bp After Masking: 9354118 bp Masked: 6.59 % -- Input Database Coverage: 10124832 bp out of 1066804524 bp ( 0.95 % ) Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:10 (hh:mm:ss) Elapsed Time, 940 HSPs Collected Number of families returned by RECON: 303 Round Time: 00:03:39 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7596 repeats masked totaling 1828592 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30229590 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30031741 bp After Masking: 27783239 bp Masked: 7.49 % -- Input Database Coverage: 40354422 bp out of 1066804524 bp ( 3.78 % ) Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:16:01 (hh:mm:ss) Elapsed Time, 6436 HSPs Collected Number of families returned by RECON: 1898 Round Time: 00:17:33 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23347 repeats masked totaling 5511690 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91094527 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90005501 bp After Masking: 82955708 bp Masked: 7.83 % -- Input Database Coverage: 131448949 bp out of 1066804524 bp ( 12.32 % ) Sampling Time: 00:04:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2604903 Comparison Time: 01:48:32 (hh:mm:ss) Elapsed Time, 52611 HSPs Collected Number of families returned by RECON: 12154 Round Time: 01:54:26 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77145 repeats masked totaling 19052329 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273187726 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 270016823 bp After Masking: 247132369 bp Masked: 8.48 % -- Input Database Coverage: 404636675 bp out of 1066804524 bp ( 37.93 % ) Sampling Time: 00:12:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23437281 Comparison Time: 14:04:04 (hh:mm:ss) Elapsed Time, 252566 HSPs Collected Number of families returned by RECON: 80569 Round Time: 14:48:29 (hh:mm:ss) Elapsed Time : 230 families discovered. RepeatScout/RECON discovery complete: 430 families found Classification Time: 00:14:03 (hh:mm:ss) Elapsed Time Program Time: 17:27:49 (hh:mm:ss) Elapsed Time