# 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..49]--> unknown_A (51) <--[1..2]--> unknown_B (23) <--[0..3]--> unknown_C (16) <--[0..4]--> unknown_D (67) <--[0..13]--> unknown_E (29) <--[0..2]--> unknown_F (30) <--[1..4]--> unknown_G (18) <--[2..85]--> unknown_H (15) <--[0..1]--> unknown_I (23) <--[0..18]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3228420180911_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 = 16469, name = Contig32284) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig32284	AUGUSTUS	gene	6906	7801	0.33	+	.	g1
Contig32284	AUGUSTUS	transcript	6906	7801	0.33	+	.	g1.t1
Contig32284	AUGUSTUS	start_codon	6906	6908	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig32284	AUGUSTUS	intron	6969	7440	0.49	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig32284	AUGUSTUS	intron	7505	7697	0.67	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig32284	AUGUSTUS	CDS	6906	6968	0.42	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig32284	AUGUSTUS	CDS	7441	7504	0.76	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig32284	AUGUSTUS	CDS	7698	7801	0.65	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig32284	AUGUSTUS	stop_codon	7799	7801	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgggatggaatggtgaggatctgtttctccaggaaaaacaaaacaatcggagcgtccttcaggtttaccaaagtatta
# gaattactggagaagaattacaggacacactgctccctgaaatctgtgctgcagattttgatgtaaaggagaaaataacagaaatattggagaaggga
# gacttcgacaaaaaacgagcgaggacaatggacatagatgactttcttgggtaa]
# protein sequence = [MGWNGEDLFLQEKQNNRSVLQVYQSIRITGEELQDTLLPEICAADFDVKEKITEILEKGDFDKKRARTMDIDDFLG]
# end gene g1
###
# start gene g2
Contig32284	AUGUSTUS	gene	11615	13225	0.25	-	.	g2
Contig32284	AUGUSTUS	transcript	11615	13225	0.25	-	.	g2.t1
Contig32284	AUGUSTUS	stop_codon	11615	11617	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig32284	AUGUSTUS	intron	11733	12515	0.51	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig32284	AUGUSTUS	intron	12710	12980	0.99	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig32284	AUGUSTUS	intron	13068	13168	0.99	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig32284	AUGUSTUS	CDS	11615	11732	0.25	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig32284	AUGUSTUS	CDS	12516	12709	0.99	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig32284	AUGUSTUS	CDS	12981	13067	0.99	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig32284	AUGUSTUS	CDS	13169	13225	0.99	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig32284	AUGUSTUS	start_codon	13223	13225	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggaagaaacaaacacagtccttttggatataaaacagaaagcagagaaatgcaagagcacacaagagaaagaaaaaa
# ggaaagaagaggctaaagaacgaaaagaattagccgagcacaagaaacttataacaacaattcagagtcgtggtatctggctggctggactagctgac
# aaaggttatgacccccttctcttcacaaatgtggagttgcacaatcctagtggagccaaggtttatgttgatgggaacgacactctacactggcctgt
# gttgtttatgtatccggagcacacacagacagactatatagaggacttcaacgaaaacaacacatggttgtttcatccttgcagatttcacgatcatt
# tactgcacatgtttggcccggatgtaccgcctgcttcctgggatctggacaaaaagtacaaacccgacagcttcctggtatga]
# protein sequence = [MEETNTVLLDIKQKAEKCKSTQEKEKRKEEAKERKELAEHKKLITTIQSRGIWLAGLADKGYDPLLFTNVELHNPSGA
# KVYVDGNDTLHWPVLFMYPEHTQTDYIEDFNENNTWLFHPCRFHDHLLHMFGPDVPPASWDLDKKYKPDSFLV]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370LFI.prfl --predictionStart=0  --predictionEnd=26372  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3228420180911_busco_2432604931_.temp