RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.bddOIF/RM_1428446.SatDec70645232024 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: 1733582723 Database = /scratch/tmp/rModeler.bddOIF/GCA_964188375.1_bButBut1.hap2.1 - Sequences = 458 - Bases = 1330554072 - N50 = 46619727 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 83704875-89683724 | [ 2 ] 77726027-83704875 | [ 2 ] 71747179-77726027 | [ ] 65768330-71747178 | [ 1 ] 59789482-65768330 | [ ] 53810634-59789482 | [ 2 ] 47831786-53810634 | [ ] 41852937-47831785 | [ 6 ] 35874089-41852937 | [ 1 ] 29895241-35874089 | [ 6 ] 23916393-29895241 | [ 3 ] 17937544-23916392 | [ 3 ] 11958696-17937544 | [ 2 ] 5979848-11958696 | [ 3 ] 1000-5979848 |************************************************** [ 427 ] Storage Throughput = excellent ( 1626.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012116 bp ( 40008916 non ambiguous ) - Num Contigs Represented = 93 - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:50 (hh:mm:ss) Elapsed Time Round Time: 00:10:27 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (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... 1360 repeats masked totaling 519484 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032630 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10032430 bp After Masking: 8838988 bp Masked: 11.90 % -- Input Database Coverage: 10032630 bp out of 1330554072 bp ( 0.75 % ) Sampling Time: 00:02:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:03 (hh:mm:ss) Elapsed Time, 770 HSPs Collected Number of families returned by RECON: 276 Round Time: 00:05:38 (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 : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4295 repeats masked totaling 1661865 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019565 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 30016565 bp After Masking: 26233241 bp Masked: 12.60 % -- Input Database Coverage: 40052195 bp out of 1330554072 bp ( 3.01 % ) Sampling Time: 00:02:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:14:27 (hh:mm:ss) Elapsed Time, 5459 HSPs Collected Number of families returned by RECON: 1482 Round Time: 00:17:27 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13708 repeats masked totaling 4757147 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023446 bp Num Contigs Represented = 144 Non ambiguous bp: Initial: 90017246 bp After Masking: 77943511 bp Masked: 13.41 % -- Input Database Coverage: 130075641 bp out of 1330554072 bp ( 9.78 % ) Sampling Time: 00:12:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 01:27:15 (hh:mm:ss) Elapsed Time, 39806 HSPs Collected Number of families returned by RECON: 8238 Round Time: 01:42:30 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:38:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56875 repeats masked totaling 18852566 bp(s). - TE Masking time 00:01:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046599 bp Num Contigs Represented = 249 Non ambiguous bp: Initial: 270026060 bp After Masking: 230912646 bp Masked: 14.49 % -- Input Database Coverage: 400122240 bp out of 1330554072 bp ( 30.07 % ) Sampling Time: 00:43:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 10:58:18 (hh:mm:ss) Elapsed Time, 225691 HSPs Collected Number of families returned by RECON: 52243 Round Time: 11:58:27 (hh:mm:ss) Elapsed Time : 241 families discovered. RepeatScout/RECON discovery complete: 377 families found Classification Time: 00:20:09 (hh:mm:ss) Elapsed Time Program Time: 14:34:38 (hh:mm:ss) Elapsed Time