RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/genbankBuild/GCA/025/265/405/GCA_025265405.1_mMesDen1_primary_haplotype/trackData/repeatModeler/RM_114499.SunDec252031142022 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: 1672029073 Database = /hive/data/genomes/asmHubs/genbankBuild/GCA/025/265/405/GCA_025265405.1_mMesDen1_primary_haplotype/trackData/repeatModeler/GCA_025265405.1_mMesDen1_primary_haplotype - Sequences = 73 - Bases = 2683375131 Storage Throughput = good ( 971.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028994 bp ( 40028794 non ambiguous ) - Num Contigs Represented = 42 - Sequence extraction : 00:02:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:28 (hh:mm:ss) Elapsed Time Round Time: 00:30:52 (hh:mm:ss) Elapsed Time : 197 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10574 repeats masked totaling 3102994 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034198 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10033998 bp After Masking: 6522036 bp Masked: 35.00 % -- Input Database Coverage: 10034198 bp out of 2683375131 bp ( 0.37 % ) Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:36 (hh:mm:ss) Elapsed Time, 14518 HSPs Collected Number of families returned by RECON: 754 Round Time: 00:07:57 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32949 repeats masked totaling 9535090 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034795 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30034795 bp After Masking: 18899263 bp Masked: 37.08 % -- Input Database Coverage: 40068993 bp out of 2683375131 bp ( 1.49 % ) Sampling Time: 00:04:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:24:50 (hh:mm:ss) Elapsed Time, 36180 HSPs Collected Number of families returned by RECON: 2558 Round Time: 00:32:38 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111567 repeats masked totaling 32286734 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017024 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 90017024 bp After Masking: 54512409 bp Masked: 39.44 % -- Input Database Coverage: 130086017 bp out of 2683375131 bp ( 4.85 % ) Sampling Time: 00:12:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:23:02 (hh:mm:ss) Elapsed Time, 99371 HSPs Collected Number of families returned by RECON: 8979 Round Time: 02:46:39 (hh:mm:ss) Elapsed Time : 188 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 384475 repeats masked totaling 107939628 bp(s). - TE Masking time 00:04:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270050687 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 270027685 bp After Masking: 151895385 bp Masked: 43.75 % -- Input Database Coverage: 400136704 bp out of 2683375131 bp ( 14.91 % ) Sampling Time: 00:36:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 15:42:29 (hh:mm:ss) Elapsed Time, 372818 HSPs Collected Number of families returned by RECON: 29547 Round Time: 16:59:10 (hh:mm:ss) Elapsed Time : 326 families discovered. RepeatScout/RECON discovery complete: 782 families found Classification Time: 00:36:44 (hh:mm:ss) Elapsed Time Program Time: 21:34:00 (hh:mm:ss) Elapsed Time