RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Jye38c/RM_3986.FriJul191043162024 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: 1721410991 Database = /dev/shm/rModeler.Jye38c/GCF_014805685.1_ASM1480568v1 - Sequences = 286 - Bases = 742596447 - N50 = 28481530 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 39553619-42378593 | [ 1 ] 36728646-39553619 | [ ] 33903673-36728646 | [ 3 ] 31078700-33903673 | [ 1 ] 28253727-31078700 |* [ 6 ] 25428754-28253727 | [ 4 ] 22603781-25428754 | [ 3 ] 19778807-22603780 | [ 2 ] 16953834-19778807 |* [ 7 ] 14128861-16953834 | [ 1 ] 11303888-14128861 | [ 1 ] 8478915-11303888 | [ ] 5653942-8478915 | [ ] 2828969-5653942 | [ ] 3996-2828969 |************************************************** [ 257 ] Storage Throughput = excellent ( 1042.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40107328 bp ( 40034470 non ambiguous ) - Num Contigs Represented = 42 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:40 (hh:mm:ss) Elapsed Time Round Time: 00:34:46 (hh:mm:ss) Elapsed Time : 558 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13421 repeats masked totaling 2516027 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10075311 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10023744 bp After Masking: 6862573 bp Masked: 31.54 % -- Input Database Coverage: 10075311 bp out of 742596447 bp ( 1.36 % ) Sampling Time: 00:02:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:24:05 (hh:mm:ss) Elapsed Time, 5919 HSPs Collected Number of families returned by RECON: 986 Round Time: 00:26:56 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39735 repeats masked totaling 7656109 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032007 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30010716 bp After Masking: 20532466 bp Masked: 31.58 % -- Input Database Coverage: 40107318 bp out of 742596447 bp ( 5.40 % ) Sampling Time: 00:05:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 01:19:20 (hh:mm:ss) Elapsed Time, 32220 HSPs Collected Number of families returned by RECON: 3602 Round Time: 01:26:57 (hh:mm:ss) Elapsed Time : 83 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 128023 repeats masked totaling 24217978 bp(s). - TE Masking time 00:02:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90241295 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 90004826 bp After Masking: 60256678 bp Masked: 33.05 % -- Input Database Coverage: 130348613 bp out of 742596447 bp ( 17.55 % ) Sampling Time: 00:17:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 07:07:53 (hh:mm:ss) Elapsed Time, 155257 HSPs Collected Number of families returned by RECON: 12313 Round Time: 07:37:06 (hh:mm:ss) Elapsed Time : 317 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:41:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 430693 repeats masked totaling 82064338 bp(s). - TE Masking time 00:10:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270310129 bp Num Contigs Represented = 137 Non ambiguous bp: Initial: 270031223 bp After Masking: 171451385 bp Masked: 36.51 % -- Input Database Coverage: 400658742 bp out of 742596447 bp ( 53.95 % ) Sampling Time: 00:56:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23396220 Comparison Time: 33:53:55 (hh:mm:ss) Elapsed Time, 589592 HSPs Collected Number of families returned by RECON: 46484 Round Time: 35:57:02 (hh:mm:ss) Elapsed Time : 878 families discovered. RepeatScout/RECON discovery complete: 1847 families found Classification Time: 01:28:37 (hh:mm:ss) Elapsed Time Program Time: 47:31:25 (hh:mm:ss) Elapsed Time