RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/refseqBuild/GCF/905/163/445/GCF_905163445.1_ilParAegt1.1/trackData/repeatModeler/RM_12570.MonDec262315202022 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: 1672125319 Database = /hive/data/genomes/asmHubs/refseqBuild/GCF/905/163/445/GCF_905163445.1_ilParAegt1.1/trackData/repeatModeler/GCF_905163445.1_ilParAegt1.1 - Sequences = 70 - Bases = 516571003 Storage Throughput = good ( 738.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034745 bp ( 40034545 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:10 (hh:mm:ss) Elapsed Time Round Time: 00:28:42 (hh:mm:ss) Elapsed Time : 587 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23092 repeats masked totaling 3818145 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004357 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10004157 bp After Masking: 6052247 bp Masked: 39.50 % -- Input Database Coverage: 10004357 bp out of 516571003 bp ( 1.94 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:31 (hh:mm:ss) Elapsed Time, 4316 HSPs Collected Number of families returned by RECON: 1020 Round Time: 00:08:14 (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 : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 69598 repeats masked totaling 11703581 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030308 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30030308 bp After Masking: 17982245 bp Masked: 40.12 % -- Input Database Coverage: 40034665 bp out of 516571003 bp ( 7.75 % ) Sampling Time: 00:02:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:33:22 (hh:mm:ss) Elapsed Time, 32103 HSPs Collected Number of families returned by RECON: 3514 Round Time: 00:41:05 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 219624 repeats masked totaling 35549788 bp(s). - TE Masking time 00:02:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011964 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 90011764 bp After Masking: 53196581 bp Masked: 40.90 % -- Input Database Coverage: 130046629 bp out of 516571003 bp ( 25.17 % ) Sampling Time: 00:08:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 03:43:20 (hh:mm:ss) Elapsed Time, 171989 HSPs Collected Number of families returned by RECON: 10057 Round Time: 04:19:06 (hh:mm:ss) Elapsed Time : 454 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 720714 repeats masked totaling 117248223 bp(s). - TE Masking time 00:14:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270003183 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 270002149 bp After Masking: 148949420 bp Masked: 44.83 % -- Input Database Coverage: 400049812 bp out of 516571003 bp ( 77.44 % ) Sampling Time: 00:32:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22885995 Comparison Time: 27:51:13 (hh:mm:ss) Elapsed Time, 440189 HSPs Collected Number of families returned by RECON: 31058 Round Time: 30:01:28 (hh:mm:ss) Elapsed Time : 963 families discovered. RepeatScout/RECON discovery complete: 2116 families found Classification Time: 01:19:42 (hh:mm:ss) Elapsed Time Program Time: 36:58:17 (hh:mm:ss) Elapsed Time