RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MMVkMd/RM_504510.ThuJul252220312024 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: 1721971222 Database = /dev/shm/rModeler.MMVkMd/GCF_021917145.1_fHypTra1 - Sequences = 376 - Bases = 437273953 - N50 = 14953238 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 21165213-22675904 | [ 2 ] 19654522-21165212 | [ 1 ] 18143832-19654522 | [ ] 16633141-18143831 | [ 3 ] 15122451-16633141 | [ 2 ] 13611760-15122450 |* [ 7 ] 12101069-13611759 | [ 1 ] 10590379-12101069 | [ 3 ] 9079688-10590378 | [ 2 ] 7568998-9079688 | [ 1 ] 6058307-7568997 | [ 2 ] 4547616-6058306 | [ 2 ] 3036926-4547616 | [ 3 ] 1526235-3036925 |* [ 7 ] 15545-1526235 |************************************************** [ 340 ] Storage Throughput = good ( 752.21 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40052971 bp ( 40024225 non ambiguous ) - Num Contigs Represented = 143 - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:29 (hh:mm:ss) Elapsed Time Round Time: 00:54:33 (hh:mm:ss) Elapsed Time : 487 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6420 repeats masked totaling 1719938 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026114 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 10020214 bp After Masking: 7540673 bp Masked: 24.75 % -- Input Database Coverage: 10026114 bp out of 437273953 bp ( 2.29 % ) Sampling Time: 00:01:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 01:25:21 (hh:mm:ss) Elapsed Time, 12330 HSPs Collected Number of families returned by RECON: 1303 Round Time: 01:30:47 (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 : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19416 repeats masked totaling 5347581 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026825 bp Num Contigs Represented = 122 Non ambiguous bp: Initial: 30003979 bp After Masking: 22687848 bp Masked: 24.38 % -- Input Database Coverage: 40052939 bp out of 437273953 bp ( 9.16 % ) Sampling Time: 00:04:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 04:45:37 (hh:mm:ss) Elapsed Time, 52607 HSPs Collected Number of families returned by RECON: 5514 Round Time: 04:56:16 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 63446 repeats masked totaling 16722466 bp(s). - TE Masking time 00:02:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90074624 bp Num Contigs Represented = 217 Non ambiguous bp: Initial: 90000457 bp After Masking: 67248406 bp Masked: 25.28 % -- Input Database Coverage: 130127563 bp out of 437273953 bp ( 29.76 % ) Sampling Time: 00:18:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2611755 Comparison Time: 14:06:38 (hh:mm:ss) Elapsed Time, 257652 HSPs Collected Number of families returned by RECON: 19731 Round Time: 14:50:53 (hh:mm:ss) Elapsed Time : 340 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 232959 repeats masked totaling 61719062 bp(s). - TE Masking time 00:08:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270219815 bp Num Contigs Represented = 355 Non ambiguous bp: Initial: 270003528 bp After Masking: 190450127 bp Masked: 29.46 % -- Input Database Coverage: 400347378 bp out of 437273953 bp ( 91.56 % ) Sampling Time: 00:38:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23711941 Comparison Time: 27:20:01 (hh:mm:ss) Elapsed Time, 1159167 HSPs Collected Number of families returned by RECON: 78663 Round Time: 29:50:41 (hh:mm:ss) Elapsed Time : 889 families discovered. RepeatScout/RECON discovery complete: 1779 families found Classification Time: 01:38:13 (hh:mm:ss) Elapsed Time Program Time: 53:41:23 (hh:mm:ss) Elapsed Time