RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.XYXGKe/RM_4004991.ThuNov141044252024 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: 1731609864 Database = /scratch/tmp/rModeler.XYXGKe/GCA_964188315.1_rPodMur119.hap1.1 - Sequences = 185 - Bases = 1522641370 - N50 = 101770169 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 128119898-137271248 | [ 1 ] 118968548-128119897 | [ 2 ] 109817198-118968547 | [ ] 100665848-109817197 | [ 3 ] 91514498-100665847 | [ 2 ] 82363148-91514497 | [ 1 ] 73211798-82363147 | [ 1 ] 64060449-73211798 | [ 1 ] 54909099-64060448 | [ 3 ] 45757749-54909098 | [ 1 ] 36606399-45757748 | [ 3 ] 27455049-36606398 | [ 1 ] 18303699-27455048 | [ ] 9152349-18303698 | [ 1 ] 1000-9152349 |************************************************** [ 165 ] Storage Throughput = excellent ( 1454.61 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029389 bp ( 40025789 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:45 (hh:mm:ss) Elapsed Time Round Time: 00:11:02 (hh:mm:ss) Elapsed Time : 581 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18537 repeats masked totaling 3318398 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006872 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10005672 bp After Masking: 6503885 bp Masked: 35.00 % -- Input Database Coverage: 10006872 bp out of 1522641370 bp ( 0.66 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:53 (hh:mm:ss) Elapsed Time, 7890 HSPs Collected Number of families returned by RECON: 1251 Round Time: 00:03:41 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57544 repeats masked totaling 10259751 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022514 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30020114 bp After Masking: 18710918 bp Masked: 37.67 % -- Input Database Coverage: 40029386 bp out of 1522641370 bp ( 2.63 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:12:34 (hh:mm:ss) Elapsed Time, 38202 HSPs Collected Number of families returned by RECON: 4294 Round Time: 00:14:46 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 183240 repeats masked totaling 32296619 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042041 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90031133 bp After Masking: 54226137 bp Masked: 39.77 % -- Input Database Coverage: 130071427 bp out of 1522641370 bp ( 8.54 % ) Sampling Time: 00:04:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:08:28 (hh:mm:ss) Elapsed Time, 284783 HSPs Collected Number of families returned by RECON: 13668 Round Time: 01:19:00 (hh:mm:ss) Elapsed Time : 434 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 616028 repeats masked totaling 108247418 bp(s). - TE Masking time 00:03:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270038925 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 270008838 bp After Masking: 152774364 bp Masked: 43.42 % -- Input Database Coverage: 400110352 bp out of 1522641370 bp ( 26.28 % ) Sampling Time: 00:14:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 08:16:37 (hh:mm:ss) Elapsed Time, 1001127 HSPs Collected Number of families returned by RECON: 47065 Round Time: 09:00:19 (hh:mm:ss) Elapsed Time : 1046 families discovered. RepeatScout/RECON discovery complete: 2204 families found Classification Time: 00:34:48 (hh:mm:ss) Elapsed Time Program Time: 11:23:36 (hh:mm:ss) Elapsed Time