# 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..444]--> unknown_A (29) <--[0..17]--> unknown_B (7) <--[0..11]--> unknown_C (15) <--[0..1]--> unknown_D (31) <--[0..1]--> unknown_E (18) <--[2..19]--> unknown_F (25) <--[6..16]--> unknown_G (25) <--[0..81]--> unknown_H (10) <--[0..3]--> unknown_I (14) <--[0..626]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6094920180911_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 = 6134, name = Contig60949) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig60949	AUGUSTUS	gene	3347	5535	0.57	-	.	g1
Contig60949	AUGUSTUS	transcript	3347	5535	0.57	-	.	g1.t1
Contig60949	AUGUSTUS	stop_codon	3347	3349	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig60949	AUGUSTUS	intron	3461	5061	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig60949	AUGUSTUS	intron	5251	5451	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig60949	AUGUSTUS	CDS	3347	3460	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig60949	AUGUSTUS	CDS	5062	5250	0.97	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig60949	AUGUSTUS	CDS	5452	5535	0.57	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig60949	AUGUSTUS	start_codon	5533	5535	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaaaaccctgttggagggagggactacgttgattgtggacagatacgcattctcgggagtcgcgtttactgctgcca
# aacagggctttacgatagactggtgtaaacagccagacattggtctgccacggccagacctcgttcttttcctcaacctaagtcctgatgctgcggcc
# aagcggggaacgtttggcaacgagaggtatgaacagacagaattccaggtcaaggtcgcaaacaacttcttacaactgaaggaaccctactggcagga
# aattaatgcagacaaaccagagactgacctgacagcagagctgaaagacattgtgttgaacgttatctccagtgtaggggaagcgccgctgaaaaggc
# tgtggtgtgactaa]
# protein sequence = [MKTLLEGGTTLIVDRYAFSGVAFTAAKQGFTIDWCKQPDIGLPRPDLVLFLNLSPDAAAKRGTFGNERYEQTEFQVKV
# ANNFLQLKEPYWQEINADKPETDLTAELKDIVLNVISSVGEAPLKRLWCD]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370TH4.prfl --predictionStart=0  --predictionEnd=25247  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6094920180911_busco_2432604931_.temp