# 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
# --[14..1237]--> unknown_B (40) <--[1..2]--> unknown_C (22) <--[17..88]--> unknown_F (28) <--[0..12]--> unknown_G (16) <--[1..20]--> unknown_H (11) <--[2..85]--> unknown_I (23) <--[0..1]--> unknown_J (48) <--[8..66]--> unknown_K (22) <--[0..68]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3397020180911_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 = 23524, name = Contig33970) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig33970	AUGUSTUS	gene	1	7091	0.07	-	.	g1
Contig33970	AUGUSTUS	transcript	1	7091	0.07	-	.	g1.t1
Contig33970	AUGUSTUS	intron	1	2415	0.52	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig33970	AUGUSTUS	intron	2534	3031	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig33970	AUGUSTUS	intron	3247	4320	0.68	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig33970	AUGUSTUS	intron	4419	6788	0.15	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig33970	AUGUSTUS	intron	6866	6971	0.63	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig33970	AUGUSTUS	CDS	2416	2533	0.89	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig33970	AUGUSTUS	CDS	3032	3246	0.95	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig33970	AUGUSTUS	CDS	4321	4418	0.44	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig33970	AUGUSTUS	CDS	6789	6865	0.18	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig33970	AUGUSTUS	CDS	6972	7091	0.81	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig33970	AUGUSTUS	start_codon	7089	7091	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcggcaaattttttgagacaaaactcggtgcccgacaaacttgaggaacagagagcagcggtgacagatttcattg
# aacaccaaaaaactttggatcgtaaagttgttcttgtcactagcggaggaaccacggtgccgttggagagtaaaactgtgaggtttatagacaacttc
# agtgtagggtctagaggcgcaaaccgatccctgaagccatttctacgtcatttgtccgggcacaattttctggatttgttgcagctggatagggataa
# atcagactcatctgtcacagtgaaaccggaacatcaaaagcagctgtcgtccattttgcatgactatgagcgagtccagacagacaggtccctgctgt
# acgtcgagttccagaccctgtcggagtatttacacctgctacaggtgtgctccacctgtctacagagtctgggaaggtcggccatgttgtacctagca
# gcagccgtggccgacttctatatccccaaaaatgaaatgccagagcataaaatccagtcctcagacggccctctacagttgtctctacagcttgttcc
# aaaaatgttggagccactggtgaaggagtgggccacaggcttacgtcgtgtcattcaaa]
# protein sequence = [MAANFLRQNSVPDKLEEQRAAVTDFIEHQKTLDRKVVLVTSGGTTVPLESKTVRFIDNFSVGSRGANRSLKPFLRHLS
# GHNFLDLLQLDRDKSDSSVTVKPEHQKQLSSILHDYERVQTDRSLLYVEFQTLSEYLHLLQVCSTCLQSLGRSAMLYLAAAVADFYIPKNEMPEHKIQ
# SSDGPLQLSLQLVPKMLEPLVKEWATGLRRVIQ]
# end gene g1
###
# start gene g2
Contig33970	AUGUSTUS	gene	10805	13118	0.47	+	.	g2
Contig33970	AUGUSTUS	transcript	10805	13118	0.47	+	.	g2.t1
Contig33970	AUGUSTUS	start_codon	10805	10807	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig33970	AUGUSTUS	intron	10858	11836	0.56	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig33970	AUGUSTUS	intron	12236	12973	0.86	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig33970	AUGUSTUS	CDS	10805	10857	0.85	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig33970	AUGUSTUS	CDS	11837	12235	0.56	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig33970	AUGUSTUS	CDS	12974	13118	0.94	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig33970	AUGUSTUS	stop_codon	13116	13118	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgcacagatcgtcgtccctaggatggatccacttatctctaatggttagctggcttggcagcgatactgataccgcta
# atggaaataagaagcctaataataatggaaataagaagcataataatggagataagaagcagaatgtcaataacaatacacacgactacggcggagta
# gagagtgtaagcaactcccatgagagccatgggcatggcaaaaacacgaacacaaataataaacctgctgatccaaagagcactccaaacaaacctaa
# aatccactccgatcactctaagaaaccaaacacagataacaaacagaacaaacaaaacaaacagaacaatgacaacaacaaaataaaaggaaacaaac
# aacagaccgataacagccgcagccctaatcaagtcaaaggtgcaaagaagaaccacaacgagaaaagcaacgattcgggctctggtggtaaacaacac
# ggaaacagtacctttcaacagactccacccccttctaaccagaattcgccagcgaattctagagtgcatactccaaaggcgtccggatctaaggcgtc
# cgggaataagccgcacaagcctcagtag]
# protein sequence = [MHRSSSLGWIHLSLMVSWLGSDTDTANGNKKPNNNGNKKHNNGDKKQNVNNNTHDYGGVESVSNSHESHGHGKNTNTN
# NKPADPKSTPNKPKIHSDHSKKPNTDNKQNKQNKQNNDNNKIKGNKQQTDNSRSPNQVKGAKKNHNEKSNDSGSGGKQHGNSTFQQTPPPSNQNSPAN
# SRVHTPKASGSKASGNKPHKPQ]
# end gene g2
###
# start gene g3
Contig33970	AUGUSTUS	gene	18586	21765	0.35	+	.	g3
Contig33970	AUGUSTUS	transcript	18586	21765	0.35	+	.	g3.t1
Contig33970	AUGUSTUS	start_codon	18586	18588	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig33970	AUGUSTUS	intron	18748	21630	0.57	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig33970	AUGUSTUS	CDS	18586	18747	0.63	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig33970	AUGUSTUS	CDS	21631	21765	0.47	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig33970	AUGUSTUS	stop_codon	21763	21765	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgttaaattccagaacatgtataaatcagctcgcgtgtcgcgctctgcggcggacagcctgctccactgcgcagacgc
# ctgtgatagtgtgcaccacgccgccgacgctccaatgctacggtagtactgaaacactccgcccgacgctccgaatgctacagccgcgtgtcggccgc
# tctgcggcggcagcctgctccactgcgcagacgcctgtgatatgtgcaccacgcgcgacgacctgccaagctacggttagactgaaatcactccgccg
# acgctccgaatgctacaggtag]
# protein sequence = [MLNSRTCINQLACRALRRTACSTAQTPVIVCTTPPTLQCYGSTETLRPTLRMLQPRVGRSAAAACSTAQTPVICAPRA
# TTCQATVRLKSLRRRSECYR]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370MQ0.prfl --predictionStart=0  --predictionEnd=26892  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3397020180911_busco_2432604931_.temp