RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.XhoW4p/RM_28202.SatDec70026472024 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: 1733560006 Database = /scratch/tmp/rModeler.XhoW4p/GCA_037306015.1_aRhiDor1.hap2 - Sequences = 656 - Bases = 4535323468 - N50 = 538323017 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 645266932-691356993 | [ 1 ] 599176872-645266932 | [ 1 ] 553086812-599176872 | [ ] 506996752-553086812 | [ 2 ] 460906692-506996752 | [ 2 ] 414816632-460906692 | [ ] 368726572-414816632 | [ 1 ] 322636511-368726571 | [ ] 276546451-322636511 | [ ] 230456391-276546451 | [ ] 184366331-230456391 | [ 2 ] 138276271-184366331 | [ 1 ] 92186211-138276271 | [ 1 ] 46096151-92186211 | [ ] 6091-46096151 |************************************************** [ 645 ] Storage Throughput = fair ( 602.11 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006788 bp ( 40003188 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:10:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:50 (hh:mm:ss) Elapsed Time Round Time: 00:46:24 (hh:mm:ss) Elapsed Time : 826 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:33 (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... 25691 repeats masked totaling 5219352 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006304 bp Num Contigs Represented = 15 Non ambiguous bp: Initial: 10005504 bp After Masking: 3886494 bp Masked: 61.16 % -- Input Database Coverage: 10006304 bp out of 4535323468 bp ( 0.22 % ) Sampling Time: 00:04:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:50 (hh:mm:ss) Elapsed Time, 13179 HSPs Collected Number of families returned by RECON: 1185 Round Time: 00:09:59 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80670 repeats masked totaling 16465103 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040563 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30037763 bp After Masking: 11128851 bp Masked: 62.95 % -- Input Database Coverage: 40046867 bp out of 4535323468 bp ( 0.88 % ) Sampling Time: 00:12:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:20:48 (hh:mm:ss) Elapsed Time, 50355 HSPs Collected Number of families returned by RECON: 4115 Round Time: 00:37:18 (hh:mm:ss) Elapsed Time : 105 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:22:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 252184 repeats masked totaling 52039098 bp(s). - TE Masking time 00:03:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90033980 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 90026780 bp After Masking: 30620147 bp Masked: 65.99 % -- Input Database Coverage: 130080847 bp out of 4535323468 bp ( 2.87 % ) Sampling Time: 00:36:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 01:57:50 (hh:mm:ss) Elapsed Time, 237648 HSPs Collected Number of families returned by RECON: 11329 Round Time: 02:55:45 (hh:mm:ss) Elapsed Time : 385 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:06:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 804987 repeats masked totaling 167340543 bp(s). - TE Masking time 00:14:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270064236 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 270036436 bp After Masking: 81097334 bp Masked: 69.97 % -- Input Database Coverage: 400145083 bp out of 4535323468 bp ( 8.82 % ) Sampling Time: 01:52:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 13:08:24 (hh:mm:ss) Elapsed Time, 772897 HSPs Collected Number of families returned by RECON: 31424 Round Time: 16:50:49 (hh:mm:ss) Elapsed Time : 1082 families discovered. RepeatScout/RECON discovery complete: 2420 families found Classification Time: 01:31:58 (hh:mm:ss) Elapsed Time Program Time: 22:52:13 (hh:mm:ss) Elapsed Time