RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.lZlCuG/RM_3587060.FriDec60330192024 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: 1733484619 Database = /scratch/tmp/rModeler.lZlCuG/GCA_964196065.1_bCalBor7.hap2.1 - Sequences = 249 - Bases = 1169960687 - N50 = 129082959 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 206221202-220951217 | [ 1 ] 191491188-206221202 | [ ] 176761173-191491187 | [ ] 162031159-176761173 | [ 1 ] 147301144-162031158 | [ ] 132571130-147301144 | [ ] 117841115-132571129 | [ 1 ] 103111101-117841115 | [ ] 88381086-103111100 | [ ] 73651072-88381086 | [ 1 ] 58921057-73651071 | [ ] 44191043-58921057 | [ 3 ] 29461028-44191042 | [ 2 ] 14731014-29461028 |** [ 11 ] 1000-14731014 |************************************************** [ 229 ] Storage Throughput = excellent ( 1551.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030613 bp ( 40027813 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:56 (hh:mm:ss) Elapsed Time Round Time: 00:16:45 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1157 repeats masked totaling 558998 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001310 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10001110 bp After Masking: 9255645 bp Masked: 7.45 % -- Input Database Coverage: 10001310 bp out of 1169960687 bp ( 0.85 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 872 HSPs Collected Number of families returned by RECON: 266 Round Time: 00:03:39 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4258 repeats masked totaling 2007629 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029223 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 30026623 bp After Masking: 27224258 bp Masked: 9.33 % -- Input Database Coverage: 40030533 bp out of 1169960687 bp ( 3.42 % ) Sampling Time: 00:02:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:13:57 (hh:mm:ss) Elapsed Time, 11497 HSPs Collected Number of families returned by RECON: 1337 Round Time: 00:16:15 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:17 (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... 14666 repeats masked totaling 6353797 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010762 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 90002562 bp After Masking: 81271412 bp Masked: 9.70 % -- Input Database Coverage: 130041295 bp out of 1169960687 bp ( 11.12 % ) Sampling Time: 00:05:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 01:30:22 (hh:mm:ss) Elapsed Time, 57357 HSPs Collected Number of families returned by RECON: 7734 Round Time: 01:37:17 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53139 repeats masked totaling 21020448 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270033975 bp Num Contigs Represented = 143 Non ambiguous bp: Initial: 270011375 bp After Masking: 242334652 bp Masked: 10.25 % -- Input Database Coverage: 400075270 bp out of 1169960687 bp ( 34.20 % ) Sampling Time: 00:18:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22960476 Comparison Time: 11:41:34 (hh:mm:ss) Elapsed Time, 177793 HSPs Collected Number of families returned by RECON: 52107 Round Time: 12:17:15 (hh:mm:ss) Elapsed Time : 229 families discovered. RepeatScout/RECON discovery complete: 364 families found Classification Time: 00:10:24 (hh:mm:ss) Elapsed Time Program Time: 14:41:35 (hh:mm:ss) Elapsed Time