RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WBwJYJ/RM_1547368.ThuDec71242562023 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: 1701981774 Database = /dev/shm/rModeler.WBwJYJ/GCA_963210335.1_bFalPun1.1 - Sequences = 316 - Bases = 1279277844 - N50 = 92392464 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 119190851-127704412 | [ 3 ] 110677290-119190850 | [ 1 ] 102163729-110677289 | [ ] 93650168-102163728 | [ ] 85136608-93650168 | [ 3 ] 76623047-85136607 | [ ] 68109486-76623046 | [ 1 ] 59595925-68109485 | [ 1 ] 51082364-59595924 | [ 1 ] 42568804-51082364 | [ 1 ] 34055243-42568803 | [ 2 ] 25541682-34055242 | [ 1 ] 17028121-25541681 | [ 2 ] 8514560-17028120 | [ 1 ] 1000-8514560 |************************************************* [ 299 ] Storage Throughput = good ( 978.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027996 bp ( 40025396 non ambiguous ) - Num Contigs Represented = 71 - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:33 (hh:mm:ss) Elapsed Time Round Time: 00:23:25 (hh:mm:ss) Elapsed Time : 43 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1205 repeats masked totaling 391816 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006493 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10005893 bp After Masking: 9079214 bp Masked: 9.26 % -- Input Database Coverage: 10006493 bp out of 1279277844 bp ( 0.78 % ) Sampling Time: 00:01:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:12:18 (hh:mm:ss) Elapsed Time, 648 HSPs Collected Number of families returned by RECON: 269 Round Time: 00:14:43 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3602 repeats masked totaling 1416629 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021423 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 30019423 bp After Masking: 27009690 bp Masked: 10.03 % -- Input Database Coverage: 40027916 bp out of 1279277844 bp ( 3.13 % ) Sampling Time: 00:05:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:41:57 (hh:mm:ss) Elapsed Time, 6599 HSPs Collected Number of families returned by RECON: 1442 Round Time: 00:47:23 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12386 repeats masked totaling 4098088 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009063 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 90001612 bp After Masking: 80904958 bp Masked: 10.11 % -- Input Database Coverage: 130036979 bp out of 1279277844 bp ( 10.16 % ) Sampling Time: 00:15:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 03:57:17 (hh:mm:ss) Elapsed Time, 43059 HSPs Collected Number of families returned by RECON: 8831 Round Time: 04:17:08 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51855 repeats masked totaling 17607630 bp(s). - TE Masking time 00:03:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270036495 bp Num Contigs Represented = 186 Non ambiguous bp: Initial: 270016895 bp After Masking: 236934746 bp Masked: 12.25 % -- Input Database Coverage: 400073474 bp out of 1279277844 bp ( 31.27 % ) Sampling Time: 00:48:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 30:13:27 (hh:mm:ss) Elapsed Time, 185328 HSPs Collected Number of families returned by RECON: 56197 Round Time: 31:46:16 (hh:mm:ss) Elapsed Time : 208 families discovered. RepeatScout/RECON discovery complete: 350 families found Classification Time: 00:58:07 (hh:mm:ss) Elapsed Time Program Time: 38:27:02 (hh:mm:ss) Elapsed Time