RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VVXnOl/RM_192237.FriFeb71609232025 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: 1738973336 Database = /dev/shm/rModeler.VVXnOl/GCA_964638095.1_fPorCra3.hap1.1 - Sequences = 2788 - Bases = 1630001977 - N50 = 55491621 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 122780267-131550215 | [ 2 ] 114010319-122780266 | [ ] 105240372-114010319 | [ ] 96470424-105240371 | [ 1 ] 87700476-96470423 | [ ] 78930529-87700476 | [ ] 70160581-78930528 | [ 1 ] 61390633-70160580 | [ 2 ] 52620686-61390633 | [ 5 ] 43850738-52620685 | [ 4 ] 35080790-43850737 | [ 2 ] 26310843-35080790 | [ 4 ] 17540895-26310842 | [ 8 ] 8770947-17540894 | [ 1 ] 1000-8770947 |************************************************** [ 2758 ] Storage Throughput = excellent ( 1908.06 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40053155 bp ( 40037866 non ambiguous ) - Num Contigs Represented = 165 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:57 (hh:mm:ss) Elapsed Time Round Time: 03:00:42 (hh:mm:ss) Elapsed Time : 1558 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17683 repeats masked totaling 3420945 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006872 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 10003272 bp After Masking: 4826154 bp Masked: 51.75 % -- Input Database Coverage: 10006872 bp out of 1630001977 bp ( 0.61 % ) Sampling Time: 00:02:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 01:56:38 (hh:mm:ss) Elapsed Time, 6790 HSPs Collected Number of families returned by RECON: 1727 Round Time: 02:01:39 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53898 repeats masked totaling 10586783 bp(s). - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30046276 bp Num Contigs Represented = 137 Non ambiguous bp: Initial: 30034587 bp After Masking: 14684615 bp Masked: 51.11 % -- Input Database Coverage: 40053148 bp out of 1630001977 bp ( 2.46 % ) Sampling Time: 00:04:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 05:55:54 (hh:mm:ss) Elapsed Time, 57862 HSPs Collected Number of families returned by RECON: 6003 Round Time: 06:17:49 (hh:mm:ss) Elapsed Time : 122 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 164383 repeats masked totaling 30772711 bp(s). - TE Masking time 00:02:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90049669 bp Num Contigs Represented = 330 Non ambiguous bp: Initial: 90018666 bp After Masking: 43704206 bp Masked: 51.45 % -- Input Database Coverage: 130102817 bp out of 1630001977 bp ( 7.98 % ) Sampling Time: 00:13:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2713285 Comparison Time: 17:57:51 (hh:mm:ss) Elapsed Time, 406330 HSPs Collected Number of families returned by RECON: 16458 Round Time: 20:20:53 (hh:mm:ss) Elapsed Time : 806 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 583184 repeats masked totaling 110981357 bp(s). - TE Masking time 00:06:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270107827 bp Num Contigs Represented = 786 Non ambiguous bp: Initial: 270007652 bp After Masking: 112186636 bp Masked: 58.45 % -- Input Database Coverage: 400210644 bp out of 1630001977 bp ( 24.55 % ) Sampling Time: 00:41:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24608620 Comparison Time: 32:37:23 (hh:mm:ss) Elapsed Time, 1383090 HSPs Collected Number of families returned by RECON: 44250 Round Time: 33:57:06 (hh:mm:ss) Elapsed Time : 2032 families discovered. RepeatScout/RECON discovery complete: 4524 families found Classification Time: 01:23:15 (hh:mm:ss) Elapsed Time Program Time: 67:01:24 (hh:mm:ss) Elapsed Time