RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.JGDpiX/RM_2702820.ThuMar281658252024 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: 1711670304 Database = /dev/shm/rModeler.JGDpiX/GCA_963924005.1_fProBol1.1 - Sequences = 951 - Bases = 1148224649 - N50 = 46017219 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 53250568-57054109 | [ 1 ] 49447027-53250567 | [ 7 ] 45643487-49447027 | [ 4 ] 41839946-45643486 | [ 6 ] 38036406-41839946 | [ 2 ] 34232865-38036405 | [ 2 ] 30429324-34232864 | [ 2 ] 26625784-30429324 | [ ] 22822243-26625783 | [ ] 19018703-22822243 | [ ] 15215162-19018702 | [ ] 11411621-15215161 | [ ] 7608081-11411621 | [ ] 3804540-7608080 | [ ] 1000-3804540 |************************************************** [ 927 ] Storage Throughput = excellent ( 1404.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40042427 bp ( 40027627 non ambiguous ) - Num Contigs Represented = 98 - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:01 (hh:mm:ss) Elapsed Time Round Time: 00:28:49 (hh:mm:ss) Elapsed Time : 1085 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21467 repeats masked totaling 2511496 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10043058 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 10037458 bp After Masking: 5809238 bp Masked: 42.12 % -- Input Database Coverage: 10043058 bp out of 1148224649 bp ( 0.87 % ) Sampling Time: 00:03:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:05:21 (hh:mm:ss) Elapsed Time, 8687 HSPs Collected Number of families returned by RECON: 1749 Round Time: 00:08:48 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64932 repeats masked totaling 7797290 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039289 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 30030089 bp After Masking: 16714741 bp Masked: 44.34 % -- Input Database Coverage: 40082347 bp out of 1148224649 bp ( 3.49 % ) Sampling Time: 00:09:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:24:00 (hh:mm:ss) Elapsed Time, 62757 HSPs Collected Number of families returned by RECON: 6011 Round Time: 00:34:56 (hh:mm:ss) Elapsed Time : 141 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 206520 repeats masked totaling 24541537 bp(s). - TE Masking time 00:02:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90062977 bp Num Contigs Represented = 138 Non ambiguous bp: Initial: 90034038 bp After Masking: 50308522 bp Masked: 44.12 % -- Input Database Coverage: 130145324 bp out of 1148224649 bp ( 11.33 % ) Sampling Time: 00:23:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2611755 Comparison Time: 02:23:51 (hh:mm:ss) Elapsed Time, 374543 HSPs Collected Number of families returned by RECON: 19321 Round Time: 03:03:50 (hh:mm:ss) Elapsed Time : 751 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:31:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 704885 repeats masked totaling 88317410 bp(s). - TE Masking time 00:12:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270116774 bp Num Contigs Represented = 406 Non ambiguous bp: Initial: 270038498 bp After Masking: 134482249 bp Masked: 50.20 % -- Input Database Coverage: 400262098 bp out of 1148224649 bp ( 34.86 % ) Sampling Time: 01:50:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23705055 Comparison Time: 18:11:27 (hh:mm:ss) Elapsed Time, 1395660 HSPs Collected Number of families returned by RECON: 57869 Round Time: 21:50:17 (hh:mm:ss) Elapsed Time : 1750 families discovered. RepeatScout/RECON discovery complete: 3744 families found Classification Time: 02:01:26 (hh:mm:ss) Elapsed Time Program Time: 28:08:06 (hh:mm:ss) Elapsed Time