# 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..82]--> unknown_A (24) <--[3..41]--> unknown_B (72) <--[10..41]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig59420180911_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 = 23242, name = Contig594) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig594	AUGUSTUS	gene	10596	19297	0.01	+	.	g1
Contig594	AUGUSTUS	transcript	10596	19297	0.01	+	.	g1.t1
Contig594	AUGUSTUS	tss	10596	10596	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	exon	10596	10741	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	exon	12677	12746	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	start_codon	12681	12683	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	intron	12747	18146	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	intron	18259	18829	0.01	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	CDS	12681	12746	0.05	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	CDS	18147	18258	0.01	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	exon	18147	18258	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	CDS	18830	19008	0.01	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	exon	18830	19297	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	stop_codon	19006	19008	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	tts	19297	19297	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	protein_match	12684	12746	5.32	+	0	target "unknown_A[1..21]"; target_start 1; transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	protein_match	18147	18155	2.79	+	0	target "unknown_A[22..24]"; target_start 1; transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	protein_match	18186	18258	5.71	+	0	target "unknown_B[1..25]"; target_start 35; transcript_id "g1.t1"; gene_id "g1";
Contig594	AUGUSTUS	protein_match	18830	18972	2.82	+	2	target "unknown_B[25..72]"; target_start 35; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcggacgatgagttagaagcattgagagcccaaagaatggcccagctacagtcccagtacgggggcggtgctgggc
# agccaagtcaggaggagcgtgaggagaaggcccagcagatgaaggagatgaagaattccatcctaagtcaggtccttgaccaggaggccagagcacga
# ttgaatacaatagctcttgctaaaccagaaaaggcacaacgggtggaaaacatgctgtgtcagatggctcagacaggacaaattcagaataaggtann
# nnnnnnnnnnnnnnnnnnnnnnngaattttaattgttggaaaaaattttttttgggggaaaaaaaaattttataacaattaa]
# protein sequence = [MADDELEALRAQRMAQLQSQYGGGAGQPSQEEREEKAQQMKEMKNSILSQVLDQEARARLNTIALAKPEKAQRVENML
# CQMAQTGQIQNKVXXXXXXXXXILIVGKNFFWGKKKFYNN]
# sequence of block unknown_A     1 [ADDELEALRAQRMAQLQSQYGGGA] 25
# sequence of block unknown_B    35 [KAQQMKEMKNSILSQVLDQEARARLNTIALAKPEKAQRVENMLCQMAQTGQIQNKVXXXXXXXXXILIVGKN] 107
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093715EC.prfl --predictionStart=0  --predictionEnd=38915  --species=fly ./tmp/Contig59420180911_busco_2432604931_.temp