# 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..244]--> unknown_A (26) <--[0..6]--> unknown_B (38) <--[1..8]--> unknown_C (15) <--[15..23]--> unknown_D (39) <--[1..6]--> unknown_E (19) <--[0..1]--> unknown_F (29) <--[6..13]--> unknown_H (27) <--[0..1]--> unknown_I (17) <--[5..13]--> unknown_J (30) <--[0..1]--> unknown_K (28) <--[0..1]--> unknown_L (46) <--[1..23]--> unknown_M (29) <--[1..3]--> unknown_N (12) <--[2..3]--> unknown_O (13) <--[10..15]--> unknown_Q (40) <--[1..6]--> unknown_R (31) <--[7..33]--> unknown_T (18) <--[0..17]--> unknown_U (17) <--[1..2]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig10879320180911_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 = 9560, name = Contig108793) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig108793	AUGUSTUS	gene	1	3705	0.18	+	.	g1
Contig108793	AUGUSTUS	transcript	1	3705	0.18	+	.	g1.t1
Contig108793	AUGUSTUS	intron	1	539	0.93	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig108793	AUGUSTUS	intron	755	1160	0.53	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig108793	AUGUSTUS	intron	1243	2710	0.36	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig108793	AUGUSTUS	intron	2748	3560	0.68	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig108793	AUGUSTUS	CDS	540	754	0.91	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig108793	AUGUSTUS	CDS	1161	1242	0.53	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig108793	AUGUSTUS	CDS	2711	2747	0.63	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig108793	AUGUSTUS	CDS	3561	3705	0.39	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig108793	AUGUSTUS	stop_codon	3703	3705	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtggaaatggagcggtatggagatgaagctgatgtactaattgttggaggagggccagcaggcctgtcagcagcatg
# taaacttaaactcatggctaacgagcaaggaaaggagctgagggtgtgtctggtagagaaggctgctgaaattggtattatattagaaagttatcttg
# aatatcagaaacttaggcaacagttcattgataaaagagcaccactgaagacagaggtgaaggaagacagatttgcttatctaacagaaaagggaaga
# atccctataccaatacttccagatgtggaaatggaacggtatggagtgaaggcgcgattctggctcactaacaaagttggaggtgtaatagtggcttt
# tgctcttgttgttgccgcatccatagacatattttatctggatgtttatctctatttatatcctgattttttaaggaaaatggctgtaacgctctgta
# aaccctaa]
# protein sequence = [VEMERYGDEADVLIVGGGPAGLSAACKLKLMANEQGKELRVCLVEKAAEIGIILESYLEYQKLRQQFIDKRAPLKTEV
# KEDRFAYLTEKGRIPIPILPDVEMERYGVKARFWLTNKVGGVIVAFALVVAASIDIFYLDVYLYLYPDFLRKMAVTLCKP]
# end gene g1
###
# start gene g2
Contig108793	AUGUSTUS	gene	7259	9560	0.15	+	.	g2
Contig108793	AUGUSTUS	transcript	7259	9560	0.15	+	.	g2.t1
Contig108793	AUGUSTUS	start_codon	7259	7261	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig108793	AUGUSTUS	intron	7281	8867	0.21	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig108793	AUGUSTUS	intron	8900	9019	0.98	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig108793	AUGUSTUS	intron	9164	9284	0.95	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig108793	AUGUSTUS	intron	9460	9560	0.74	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig108793	AUGUSTUS	CDS	7259	7280	0.2	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig108793	AUGUSTUS	CDS	8868	8899	0.27	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig108793	AUGUSTUS	CDS	9020	9163	0.95	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig108793	AUGUSTUS	CDS	9285	9459	0.73	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgcggaccctggacaggaaagatgagggacccctcgttgttgtgggcattgtggttggactagactataaaaatcctt
# acttgagcccatttcgagaatttcagcggttcaagcaccacccctcggtcgaaccgttattccgctcgggtaaaagaatcggctacggtgcaagagca
# ctgaatgaggggggagtgcagtccatcccaaaactgactttccctggaggttgtatgataggctgtagtccagggttcatgaatgtgcccaaaatcaa
# gggaacacacaatgccatgaagagtggccttttggcggcagaatcagtgtatgaggttgttagtgatgaggaaaaaatttcacagtcaccaaccgcag]
# protein sequence = [MRTLDRKDEGPLVVVGIVVGLDYKNPYLSPFREFQRFKHHPSVEPLFRSGKRIGYGARALNEGGVQSIPKLTFPGGCM
# IGCSPGFMNVPKIKGTHNAMKSGLLAAESVYEVVSDEEKISQSPTA]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093705VV.prfl --predictionStart=0  --predictionEnd=29434  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig10879320180911_busco_2432604931_.temp