RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5uXoOd/RM_20802.SunJul140933412024 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: 1720974819 Database = /dev/shm/rModeler.5uXoOd/GCF_004355925.1_GSC_Weel_1.0 - Sequences = 10315 - Bases = 611444226 - N50 = 5783943 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 18458296-19776732 | [ 1 ] 17139861-18458296 | [ 2 ] 15821425-17139860 | [ 3 ] 14502990-15821425 | [ ] 13184554-14502989 | [ 1 ] 11866119-13184554 | [ 2 ] 10547683-11866118 | [ 3 ] 9229248-10547683 | [ 3 ] 7910812-9229247 | [ 3 ] 6592377-7910812 | [ 6 ] 5273941-6592376 | [ 8 ] 3955506-5273941 | [ 9 ] 2637070-3955505 | [ 19 ] 1318635-2637070 | [ 33 ] 200-1318635 |************************************************** [ 10222 ] Storage Throughput = excellent ( 1019.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42885158 bp ( 40023909 non ambiguous ) - Num Contigs Represented = 895 - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:33 (hh:mm:ss) Elapsed Time Round Time: 00:22:59 (hh:mm:ss) Elapsed Time : 416 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7148 repeats masked totaling 911556 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10709836 bp Num Contigs Represented = 274 Non ambiguous bp: Initial: 10024089 bp After Masking: 8910241 bp Masked: 11.11 % -- Input Database Coverage: 10709836 bp out of 611444226 bp ( 1.75 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 89676 Comparison Time: 00:07:53 (hh:mm:ss) Elapsed Time, 7910 HSPs Collected Number of families returned by RECON: 1604 Round Time: 00:08:54 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21887 repeats masked totaling 2863638 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32215322 bp Num Contigs Represented = 698 Non ambiguous bp: Initial: 30039810 bp After Masking: 26571919 bp Masked: 11.54 % -- Input Database Coverage: 42925158 bp out of 611444226 bp ( 7.02 % ) Sampling Time: 00:01:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 816003 Comparison Time: 00:41:18 (hh:mm:ss) Elapsed Time, 53842 HSPs Collected Number of families returned by RECON: 5906 Round Time: 00:45:00 (hh:mm:ss) Elapsed Time : 123 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 81157 repeats masked totaling 10960083 bp(s). - TE Masking time 00:01:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 97197814 bp Num Contigs Represented = 1731 Non ambiguous bp: Initial: 90011428 bp After Masking: 77219856 bp Masked: 14.21 % -- Input Database Coverage: 140122972 bp out of 611444226 bp ( 22.92 % ) Sampling Time: 00:05:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 7018131 Comparison Time: 04:37:49 (hh:mm:ss) Elapsed Time, 265185 HSPs Collected Number of families returned by RECON: 21426 Round Time: 05:00:14 (hh:mm:ss) Elapsed Time : 436 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 313873 repeats masked totaling 45252400 bp(s). - TE Masking time 00:08:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 291053863 bp Num Contigs Represented = 5132 Non ambiguous bp: Initial: 270010059 bp After Masking: 219273167 bp Masked: 18.79 % -- Input Database Coverage: 431176835 bp out of 611444226 bp ( 70.52 % ) Sampling Time: 00:20:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 66395526 Comparison Time: 38:47:27 (hh:mm:ss) Elapsed Time, 849426 HSPs Collected Number of families returned by RECON: 81327 Round Time: 42:14:26 (hh:mm:ss) Elapsed Time : 1140 families discovered. RepeatScout/RECON discovery complete: 2127 families found Classification Time: 01:18:55 (hh:mm:ss) Elapsed Time Program Time: 49:50:28 (hh:mm:ss) Elapsed Time