RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VZJti4/RM_420218.SunDec30809292023 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: 1701619760 Database = /dev/shm/rModeler.VZJti4/GCF_023634085.1_bFalChe1.pri - Sequences = 283 - Bases = 1309385023 - N50 = 96473976 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 119305756-127826306 | [ 3 ] 110785206-119305755 | [ 1 ] 102264656-110785205 | [ ] 93744106-102264655 | [ 1 ] 85223557-93744106 | [ 2 ] 76703007-85223556 | [ ] 68182457-76703006 | [ 1 ] 59661907-68182456 | [ 1 ] 51141357-59661906 | [ 1 ] 42620808-51141357 | [ ] 34100258-42620807 | [ 4 ] 25579708-34100257 | [ ] 17059158-25579707 | [ 3 ] 8538608-17059157 | [ 2 ] 18059-8538608 |************************************************** [ 264 ] Storage Throughput = good ( 769.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40110026 bp ( 40039577 non ambiguous ) - Num Contigs Represented = 77 - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:59 (hh:mm:ss) Elapsed Time Round Time: 00:23:31 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1389 repeats masked totaling 418365 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10062964 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10022205 bp After Masking: 8777742 bp Masked: 12.42 % -- Input Database Coverage: 10062964 bp out of 1309385023 bp ( 0.77 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:13:09 (hh:mm:ss) Elapsed Time, 763 HSPs Collected Number of families returned by RECON: 265 Round Time: 00:14:37 (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 : 00:01:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3788 repeats masked totaling 1156720 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30046982 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 30017292 bp After Masking: 26061523 bp Masked: 13.18 % -- Input Database Coverage: 40109946 bp out of 1309385023 bp ( 3.06 % ) Sampling Time: 00:03:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:33:02 (hh:mm:ss) Elapsed Time, 5397 HSPs Collected Number of families returned by RECON: 1332 Round Time: 00:37:04 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12348 repeats masked totaling 3717127 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90235873 bp Num Contigs Represented = 121 Non ambiguous bp: Initial: 90019218 bp After Masking: 78776140 bp Masked: 12.49 % -- Input Database Coverage: 130345819 bp out of 1309385023 bp ( 9.95 % ) Sampling Time: 00:11:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 03:50:45 (hh:mm:ss) Elapsed Time, 48928 HSPs Collected Number of families returned by RECON: 8813 Round Time: 04:04:04 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48560 repeats masked totaling 14810327 bp(s). - TE Masking time 00:01:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270628962 bp Num Contigs Represented = 187 Non ambiguous bp: Initial: 270033779 bp After Masking: 233100452 bp Masked: 13.68 % -- Input Database Coverage: 400974781 bp out of 1309385023 bp ( 30.62 % ) Sampling Time: 00:36:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 29:43:22 (hh:mm:ss) Elapsed Time, 287401 HSPs Collected Number of families returned by RECON: 56150 Round Time: 33:33:51 (hh:mm:ss) Elapsed Time : 216 families discovered. RepeatScout/RECON discovery complete: 349 families found Classification Time: 00:37:18 (hh:mm:ss) Elapsed Time Program Time: 39:30:25 (hh:mm:ss) Elapsed Time