RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.kgiSOb/RM_27414.MonNov182235272024 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: 1731998126 Database = /scratch/tmp/rModeler.kgiSOb/GCF_040954835.1_fLepOcu1.hap2 - Sequences = 816 - Bases = 1200589847 - N50 = 53690625 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 73656800-78916909 | [ 3 ] 68396692-73656800 | [ ] 63136583-68396691 | [ 1 ] 57876475-63136583 | [ 4 ] 52616366-57876474 | [ 1 ] 47356258-52616366 | [ 1 ] 42096149-47356257 | [ 2 ] 36836041-42096149 | [ 2 ] 31575932-36836040 | [ 1 ] 26315824-31575932 | [ ] 21055715-26315823 | [ 3 ] 15795607-21055715 | [ 5 ] 10535498-15795606 | [ 5 ] 5275390-10535498 | [ 1 ] 15282-5275390 |************************************************** [ 787 ] Storage Throughput = fair ( 573.59 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024684 bp ( 40023484 non ambiguous ) - Num Contigs Represented = 121 - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:02 (hh:mm:ss) Elapsed Time Round Time: 00:39:55 (hh:mm:ss) Elapsed Time : 389 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8307 repeats masked totaling 2064504 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004420 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 10004420 bp After Masking: 6970032 bp Masked: 30.33 % -- Input Database Coverage: 10004420 bp out of 1200589847 bp ( 0.83 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:08:06 (hh:mm:ss) Elapsed Time, 10634 HSPs Collected Number of families returned by RECON: 795 Round Time: 00:09:56 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26873 repeats masked totaling 7056105 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30020240 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 30019040 bp After Masking: 20304740 bp Masked: 32.36 % -- Input Database Coverage: 40024660 bp out of 1200589847 bp ( 3.33 % ) Sampling Time: 00:03:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:31:37 (hh:mm:ss) Elapsed Time, 94548 HSPs Collected Number of families returned by RECON: 2805 Round Time: 00:36:53 (hh:mm:ss) Elapsed Time : 61 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 00:35:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 90709 repeats masked totaling 22835289 bp(s). - TE Masking time 00:02:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035921 bp Num Contigs Represented = 210 Non ambiguous bp: Initial: 90034321 bp After Masking: 59052867 bp Masked: 34.41 % -- Input Database Coverage: 130060581 bp out of 1200589847 bp ( 10.83 % ) Sampling Time: 00:39:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 03:33:25 (hh:mm:ss) Elapsed Time, 352870 HSPs Collected Number of families returned by RECON: 8310 Round Time: 04:22:43 (hh:mm:ss) Elapsed Time : 288 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 311817 repeats masked totaling 79676304 bp(s). - TE Masking time 00:09:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270037063 bp Num Contigs Represented = 441 Non ambiguous bp: Initial: 270034063 bp After Masking: 167238821 bp Masked: 38.07 % -- Input Database Coverage: 400097644 bp out of 1200589847 bp ( 33.33 % ) Sampling Time: 00:35:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23423590 Comparison Time: 25:58:51 (hh:mm:ss) Elapsed Time, 2919735 HSPs Collected Number of families returned by RECON: 30132 Round Time: 27:45:35 (hh:mm:ss) Elapsed Time : 630 families discovered. RepeatScout/RECON discovery complete: 1383 families found Classification Time: 01:22:30 (hh:mm:ss) Elapsed Time Program Time: 34:57:32 (hh:mm:ss) Elapsed Time