RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/refseqBuild/GCF/024/166/365/GCF_024166365.1_mEleMax1_primary_haplotype/trackData/repeatModeler/RM_7188.SunDec252115432022 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: 1672031742 Database = /hive/data/genomes/asmHubs/refseqBuild/GCF/024/166/365/GCF_024166365.1_mEleMax1_primary_haplotype/trackData/repeatModeler/GCF_024166365.1_mEleMax1_primary_haplotype - Sequences = 64 - Bases = 3401247148 Storage Throughput = good ( 832.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40004316 bp ( 40004103 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:03:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:36 (hh:mm:ss) Elapsed Time Round Time: 00:29:32 (hh:mm:ss) Elapsed Time : 238 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13903 repeats masked totaling 4226785 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000656 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10000643 bp After Masking: 5489546 bp Masked: 45.11 % -- Input Database Coverage: 10000656 bp out of 3401247148 bp ( 0.29 % ) Sampling Time: 00:03:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:01 (hh:mm:ss) Elapsed Time, 45116 HSPs Collected Number of families returned by RECON: 825 Round Time: 00:10:12 (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 : 00:02:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45998 repeats masked totaling 13804583 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003655 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30003455 bp After Masking: 15630560 bp Masked: 47.90 % -- Input Database Coverage: 40004311 bp out of 3401247148 bp ( 1.18 % ) Sampling Time: 00:06:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:25:21 (hh:mm:ss) Elapsed Time, 100059 HSPs Collected Number of families returned by RECON: 1996 Round Time: 00:33:58 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 142824 repeats masked totaling 41580516 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041477 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 90000661 bp After Masking: 46425271 bp Masked: 48.42 % -- Input Database Coverage: 130045788 bp out of 3401247148 bp ( 3.82 % ) Sampling Time: 00:21:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:27:06 (hh:mm:ss) Elapsed Time, 1395315 HSPs Collected Number of families returned by RECON: 6897 Round Time: 03:01:13 (hh:mm:ss) Elapsed Time : 152 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:43:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 470887 repeats masked totaling 132766937 bp(s). - TE Masking time 00:04:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270385619 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 270024697 bp After Masking: 129702872 bp Masked: 51.97 % -- Input Database Coverage: 400431407 bp out of 3401247148 bp ( 11.77 % ) Sampling Time: 01:09:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 17:21:56 (hh:mm:ss) Elapsed Time, 19353807 HSPs Collected Number of families returned by RECON: 25054 Round Time: 19:23:20 (hh:mm:ss) Elapsed Time : 391 families discovered. RepeatScout/RECON discovery complete: 857 families found Classification Time: 00:30:27 (hh:mm:ss) Elapsed Time Program Time: 24:08:42 (hh:mm:ss) Elapsed Time