RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.J4VSgE/RM_670794.SatJul190124372025 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: 1752913475 Database = /dev/shm/rModeler.J4VSgE/GCA_048537235.1_ASM4853723v1 - Sequences = 461 - Bases = 707857291 - N50 = 28846602 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 38966274-41749142 | [ 1 ] 36183407-38966274 | [ 1 ] 33400540-36183407 | [ 1 ] 30617672-33400539 | [ 3 ] 27834805-30617672 | [ 7 ] 25051938-27834805 | [ 4 ] 22269071-25051938 | [ 4 ] 19486203-22269070 | [ 1 ] 16703336-19486203 | [ 1 ] 13920469-16703336 | [ 1 ] 11137602-13920469 | [ ] 8354734-11137601 | [ ] 5571867-8354734 | [ ] 2789000-5571867 | [ ] 6133-2789000 |************************************************** [ 437 ] Storage Throughput = excellent ( 1766.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016513 bp ( 40011113 non ambiguous ) - Num Contigs Represented = 91 - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:45 (hh:mm:ss) Elapsed Time Round Time: 00:14:26 (hh:mm:ss) Elapsed Time : 574 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 00:02:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6502 repeats masked totaling 853481 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011011 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10010211 bp After Masking: 7740368 bp Masked: 22.68 % -- Input Database Coverage: 10011011 bp out of 707857291 bp ( 1.41 % ) Sampling Time: 00:02:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 7027 HSPs Collected Number of families returned by RECON: 1552 Round Time: 00:05:11 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20955 repeats masked totaling 2897450 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005422 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 30000822 bp After Masking: 22862804 bp Masked: 23.79 % -- Input Database Coverage: 40016433 bp out of 707857291 bp ( 5.65 % ) Sampling Time: 00:06:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:12:48 (hh:mm:ss) Elapsed Time, 50816 HSPs Collected Number of families returned by RECON: 6108 Round Time: 00:20:24 (hh:mm:ss) Elapsed Time : 105 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71922 repeats masked totaling 9793099 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042913 bp Num Contigs Represented = 133 Non ambiguous bp: Initial: 90031495 bp After Masking: 68409986 bp Masked: 24.02 % -- Input Database Coverage: 130059346 bp out of 707857291 bp ( 18.37 % ) Sampling Time: 00:17:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 01:17:02 (hh:mm:ss) Elapsed Time, 354054 HSPs Collected Number of families returned by RECON: 19950 Round Time: 01:41:32 (hh:mm:ss) Elapsed Time : 541 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:49:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 290231 repeats masked totaling 44166625 bp(s). - TE Masking time 00:03:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270077405 bp Num Contigs Represented = 275 Non ambiguous bp: Initial: 270036855 bp After Masking: 189802037 bp Masked: 29.71 % -- Input Database Coverage: 400136751 bp out of 707857291 bp ( 56.53 % ) Sampling Time: 00:55:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23430435 Comparison Time: 08:42:53 (hh:mm:ss) Elapsed Time, 939689 HSPs Collected Number of families returned by RECON: 65836 Round Time: 10:24:15 (hh:mm:ss) Elapsed Time : 1291 families discovered. RepeatScout/RECON discovery complete: 2519 families found Classification Time: 00:50:43 (hh:mm:ss) Elapsed Time Program Time: 13:36:31 (hh:mm:ss) Elapsed Time