# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. # Initialising the parameters using config directory /augustus/config/ ... # Using protein profile unknown # --[0..438]--> unknown_A (30) <--[1..2]--> unknown_B (9) <--[0..37]--> unknown_C (10) <--[0..2]--> unknown_D (39) <--[4..49]--> unknown_E (38) <--[32..77]--> unknown_I (15) <--[0..8]-- # BUSCO_20180911_busco_2432604931 version. Using default transition matrix. # admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0) # Looks like ./tmp/Contig4788920180911_busco_2432604931_.temp is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 11462, name = Contig47889) ----- # # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands # start gene g1 Contig47889 AUGUSTUS gene 7343 7732 0.4 + . g1 Contig47889 AUGUSTUS transcript 7343 7732 0.4 + . g1.t1 Contig47889 AUGUSTUS start_codon 7343 7345 . + 0 transcript_id "g1.t1"; gene_id "g1"; Contig47889 AUGUSTUS CDS 7343 7732 0.4 + 0 transcript_id "g1.t1"; gene_id "g1"; Contig47889 AUGUSTUS stop_codon 7730 7732 . + 0 transcript_id "g1.t1"; gene_id "g1"; # coding sequence = [atggctgatcacaagccaagattgtgtcaccttgtgaaatggccagattttcagggctacggatttaacttacacgcag # aaagggggaaagctgggcagttcataggaaaggtggacgagggatctccggcggaagcagcgggcctgagggagggggaccgaatcgtagaaataaat # ggtacaaatataggaaatgaaaaccaccagcaagtggtggggcggatcaagtcgcttggtgacgaggttaatctattagtggtggatccagacacgga # caagtattataaagatattaaacaaattgtgagaggtgatctcccagaagttgagaaaaggagtgcagcaagaaatgaaacccaggaaaattcagcag # gtactgaatggggataa] # protein sequence = [MADHKPRLCHLVKWPDFQGYGFNLHAERGKAGQFIGKVDEGSPAEAAGLREGDRIVEINGTNIGNENHQQVVGRIKSL # GDEVNLLVVDPDTDKYYKDIKQIVRGDLPEVEKRSAARNETQENSAGTEWG] # end gene g1 ### # command line: # /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370WWI.prfl --predictionStart=0 --predictionEnd=27594 --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4788920180911_busco_2432604931_.temp