# 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..399]--> unknown_A (17) <--[3..18]--> unknown_B (29) <--[1..8]--> unknown_C (20) <--[12..21]--> unknown_E (22) <--[0..6]--> unknown_F (15) <--[1..4]--> unknown_G (12) <--[0..6]--> unknown_H (7) <--[0..9]--> unknown_I (26) <--[0..28]--> unknown_J (87) <--[0..8]--> unknown_K (62) <--[1..2]--> unknown_L (8) <--[2..8]--> unknown_M (26) <--[4..11]--> unknown_N (39) <--[0..1]--> unknown_O (110) <--[0..8]--> unknown_P (6) <--[0..87]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig317820180911_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 = 5620, name = Contig3178) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig3178	AUGUSTUS	gene	1	5620	0.22	+	.	g1
Contig3178	AUGUSTUS	transcript	1	5620	0.22	+	.	g1.t1
Contig3178	AUGUSTUS	intron	1	2896	0.44	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3178	AUGUSTUS	intron	3071	3523	0.82	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3178	AUGUSTUS	intron	3610	5620	0.37	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3178	AUGUSTUS	CDS	2897	3070	0.6	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig3178	AUGUSTUS	exon	2897	3070	.	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig3178	AUGUSTUS	CDS	3524	3609	0.57	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig3178	AUGUSTUS	exon	3524	3609	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gtatggttaaacacatcaccggaggatacaaagtgacctatcatccggagggtcccgaggggccggcgtgggaggtgga
# ctacaccccacctttcaaacgcatcagcatgctgaaggggctggaggagaggttaggggtcacattcccaaacacggaaaagtttgactcagaaggca
# cgcgtaaatttttggatgatctatgcgttaagcatcaggttgaatgtccagctcccaggacagtggcgcgactcctggacaag]
# protein sequence = [MVKHITGGYKVTYHPEGPEGPAWEVDYTPPFKRISMLKGLEERLGVTFPNTEKFDSEGTRKFLDDLCVKHQVECPAPR
# TVARLLDK]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937066G.prfl --predictionStart=0  --predictionEnd=25476  --species=fly ./tmp/Contig317820180911_busco_2432604931_.temp