RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.Q39XCN/RM_2392828.WedNov132025192024 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: 1731558319 Database = /scratch/tmp/rModeler.Q39XCN/GCA_036873955.1_bMerOct1.hap1 - Sequences = 569 - Bases = 1245791205 - N50 = 125300045 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202233963-216678325 | [ 1 ] 187789602-202233963 | [ ] 173345241-187789602 | [ ] 158900880-173345241 | [ 1 ] 144456519-158900880 | [ ] 130012158-144456519 | [ ] 115567797-130012158 | [ 1 ] 101123436-115567797 | [ ] 86679075-101123436 | [ 1 ] 72234714-86679075 | [ 1 ] 57790353-72234714 | [ 1 ] 43345992-57790353 | [ ] 28901631-43345992 | [ 4 ] 14457270-28901631 |* [ 11 ] 12909-14457270 |************************************************* [ 548 ] Storage Throughput = excellent ( 1532.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010698 bp ( 40008473 non ambiguous ) - Num Contigs Represented = 86 - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:43 (hh:mm:ss) Elapsed Time Round Time: 00:15:17 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2299 repeats masked totaling 1019962 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008060 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10007860 bp After Masking: 8399314 bp Masked: 16.07 % -- Input Database Coverage: 10008060 bp out of 1245791205 bp ( 0.80 % ) Sampling Time: 00:02:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:57 (hh:mm:ss) Elapsed Time, 8219 HSPs Collected Number of families returned by RECON: 295 Round Time: 00:06:29 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7416 repeats masked totaling 3315627 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002624 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 30000599 bp After Masking: 24904435 bp Masked: 16.99 % -- Input Database Coverage: 40010684 bp out of 1245791205 bp ( 3.21 % ) Sampling Time: 00:05:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:19:39 (hh:mm:ss) Elapsed Time, 7111 HSPs Collected Number of families returned by RECON: 1821 Round Time: 00:25:41 (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 : 00:02:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21481 repeats masked totaling 8894796 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040944 bp Num Contigs Represented = 143 Non ambiguous bp: Initial: 90035044 bp After Masking: 75901016 bp Masked: 15.70 % -- Input Database Coverage: 130051628 bp out of 1245791205 bp ( 10.44 % ) Sampling Time: 00:14:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 02:15:08 (hh:mm:ss) Elapsed Time, 93347 HSPs Collected Number of families returned by RECON: 10533 Round Time: 02:30:49 (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 : 00:06:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:40:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80556 repeats masked totaling 31618855 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270040272 bp Num Contigs Represented = 279 Non ambiguous bp: Initial: 270026572 bp After Masking: 222263055 bp Masked: 17.69 % -- Input Database Coverage: 400091900 bp out of 1245791205 bp ( 32.12 % ) Sampling Time: 00:49:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23177836 Comparison Time: 18:38:19 (hh:mm:ss) Elapsed Time, 364382 HSPs Collected Number of families returned by RECON: 61237 Round Time: 19:52:27 (hh:mm:ss) Elapsed Time : 176 families discovered. RepeatScout/RECON discovery complete: 337 families found Classification Time: 00:15:35 (hh:mm:ss) Elapsed Time Program Time: 23:26:18 (hh:mm:ss) Elapsed Time