RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/refseqBuild/GCF/905/147/365/GCF_905147365.1_ilAriAges1.1/trackData/repeatModeler/RM_35146.MonDec262121132022 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: 1672118472 Database = /hive/data/genomes/asmHubs/refseqBuild/GCF/905/147/365/GCF_905147365.1_ilAriAges1.1/trackData/repeatModeler/GCF_905147365.1_ilAriAges1.1 - Sequences = 25 - Bases = 435265205 Storage Throughput = good ( 762.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027437 bp ( 40027437 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:51 (hh:mm:ss) Elapsed Time Round Time: 00:20:19 (hh:mm:ss) Elapsed Time : 1017 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25744 repeats masked totaling 4356369 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001653 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10001653 bp After Masking: 5546014 bp Masked: 44.55 % -- Input Database Coverage: 10001653 bp out of 435265205 bp ( 2.30 % ) Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:17 (hh:mm:ss) Elapsed Time, 4746 HSPs Collected Number of families returned by RECON: 1069 Round Time: 00:06:50 (hh:mm:ss) Elapsed Time : 10 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 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 77709 repeats masked totaling 12966504 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025704 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30025704 bp After Masking: 16691479 bp Masked: 44.41 % -- Input Database Coverage: 40027357 bp out of 435265205 bp ( 9.20 % ) Sampling Time: 00:02:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:26:05 (hh:mm:ss) Elapsed Time, 32059 HSPs Collected Number of families returned by RECON: 3294 Round Time: 00:32:01 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 237614 repeats masked totaling 38851357 bp(s). - TE Masking time 00:03:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030286 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90030286 bp After Masking: 50021337 bp Masked: 44.44 % -- Input Database Coverage: 130057643 bp out of 435265205 bp ( 29.88 % ) Sampling Time: 00:08:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 03:01:41 (hh:mm:ss) Elapsed Time, 221471 HSPs Collected Number of families returned by RECON: 9325 Round Time: 03:32:57 (hh:mm:ss) Elapsed Time : 491 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 783870 repeats masked totaling 131140181 bp(s). - TE Masking time 00:16:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039571 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270038837 bp After Masking: 135411273 bp Masked: 49.85 % -- Input Database Coverage: 400097214 bp out of 435265205 bp ( 91.92 % ) Sampling Time: 00:32:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 22:24:47 (hh:mm:ss) Elapsed Time, 667363 HSPs Collected Number of families returned by RECON: 25676 Round Time: 24:29:16 (hh:mm:ss) Elapsed Time : 1118 families discovered. RepeatScout/RECON discovery complete: 2702 families found Classification Time: 01:58:59 (hh:mm:ss) Elapsed Time Program Time: 31:00:22 (hh:mm:ss) Elapsed Time