# 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..58]--> unknown_A (27) <--[8..14]--> unknown_C (21) <--[8..26]--> unknown_E (16) <--[3..26]--> unknown_F (34) <--[2..54]--> unknown_G (28) <--[0..5]--> unknown_H (23) <--[0..50]--> unknown_I (27) <--[16..102]--> unknown_J (8) <--[9..12]--> unknown_L (16) <--[0..66]--> unknown_M (12) <--[1..194]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2685420180911_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 = 22226, name = Contig26854) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig26854	AUGUSTUS	gene	1	5477	0.15	+	.	g1
Contig26854	AUGUSTUS	transcript	1	5477	0.15	+	.	g1.t1
Contig26854	AUGUSTUS	intron	1	1828	0.58	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig26854	AUGUSTUS	intron	1913	2061	0.92	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig26854	AUGUSTUS	intron	2286	2566	0.84	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig26854	AUGUSTUS	intron	2739	5309	0.37	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig26854	AUGUSTUS	CDS	1829	1912	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig26854	AUGUSTUS	CDS	2062	2285	0.78	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig26854	AUGUSTUS	CDS	2567	2738	1	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig26854	AUGUSTUS	CDS	5310	5477	0.69	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig26854	AUGUSTUS	stop_codon	5475	5477	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gttgtgctcccatacctgaaacagaagttagatcaatggtttgaggaggcaagacataattctaacacaggtcacttac
# caaagaatcaaatgctgaagcagttatataaggtatttgtagctgcttacccgtacattcacatgagctgggagggcagtatactgatgtatcagata
# gtgtacatgtttgggaagatctcctggcactctcctcttcttcacctgtcaggaaccaggctttctcatgtagaagaggaggaggaagaatcagatag
# accaactttttctgaccagtgggcatcttcaagtgtgcctggaaagctgaatctggcggtaagaaaagtccttggtgtaacagctgtcaccctgtcca
# caggtttgtctgtgggggtgtttttcctgcagttcctggagtggtggtattccagtgaaaacaatgcaccatctctaatggccctgcctatacctgct
# cctcctaagctaatactccgagacacgcagggacatagtttaatcaaactggtacctcagattcctaacaagatccagtcaccagctatcatccagac
# agcacatttaatcaaactgtaccctcccagattcctaaacaagatccagtcaccagctatccatccagactgcagctag]
# protein sequence = [VVLPYLKQKLDQWFEEARHNSNTGHLPKNQMLKQLYKVFVAAYPYIHMSWEGSILMYQIVYMFGKISWHSPLLHLSGT
# RLSHVEEEEEESDRPTFSDQWASSSVPGKLNLAVRKVLGVTAVTLSTGLSVGVFFLQFLEWWYSSENNAPSLMALPIPAPPKLILRDTQGHSLIKLVP
# QIPNKIQSPAIIQTAHLIKLYPPRFLNKIQSPAIHPDCS]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370INZ.prfl --predictionStart=0  --predictionEnd=22226  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2685420180911_busco_2432604931_.temp