# 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
# --[2..74]--> unknown_A (12) <--[0..2]--> unknown_B (6) <--[15..33]--> unknown_D (26) <--[2..26]--> unknown_E (19) <--[18..37]--> unknown_G (19) <--[1..5]--> unknown_H (23) <--[3..29]--> unknown_I (28) <--[21..46]--> unknown_K (16) <--[0..3]--> unknown_L (28) <--[0..26]--> unknown_M (10) <--[1..1]--> unknown_N (24) <--[43..113]--> unknown_Q (22) <--[56..104]--> unknown_U (42) <--[0..3]--> unknown_V (26) <--[0..12]--> unknown_W (22) <--[1..16]--> unknown_X (28) <--[5..9]--> unknown_Y (24) <--[1..7]--> unknown_Z (12) <--[1..5]--> unknown_AA (16) <--[8..36]--> unknown_AC (61) <--[0..1]--> unknown_AD (49) <--[0..124]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4103520180911_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 = 16048, name = Contig41035) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig41035	AUGUSTUS	gene	106	7148	0.04	+	.	g1
Contig41035	AUGUSTUS	transcript	106	7148	0.04	+	.	g1.t1
Contig41035	AUGUSTUS	start_codon	106	108	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	intron	150	846	0.37	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	intron	940	1110	0.75	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	intron	1260	3325	0.33	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	intron	3430	6028	0.2	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	intron	6111	7032	0.51	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	CDS	106	149	0.64	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	CDS	847	939	0.45	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	CDS	1111	1259	0.75	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	CDS	3326	3429	0.28	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	CDS	6029	6110	0.57	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	CDS	7033	7148	0.63	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig41035	AUGUSTUS	stop_codon	7146	7148	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtatgcgtacaggtgcattgcatttgctttctccaaagagaggttggaaaaaattaaggaagaaagaaatcacgtaa
# tgtttcccgatgaaattgacactccacgggaaagggacgccaaggataggtttcaaagataccgaggactgaaaagttttaggacctcgccctgggac
# cccaaggaaaacctcccctccgactacgccaggatattccagtttaaggacttcaggaggacgaagaagagaattttgaaggatttagacgatgaggg
# agtcatggtttgcccccaatcaaatccaaaagacagactcatcttccaagtggttcggagatactcagctttccgattatttctcacagcaccaccaa
# tgcaagcaagcagtaagtgcaatgatttgacgtggttcaaaacctgctggaactgcgaaccaataggggaagacgaacggcacatcaaagaaccctta
# gaagagaatttcccaaagtggacctacaaccccacagtacttaatccacctccaacgctggagagttctcaatctatgtccacggagccatcagccta
# tcaactttttgatgattag]
# protein sequence = [MYAYRCIAFAFSKERLEKIKEERNHVMFPDEIDTPRERDAKDRFQRYRGLKSFRTSPWDPKENLPSDYARIFQFKDFR
# RTKKRILKDLDDEGVMVCPQSNPKDRLIFQVVRRYSAFRLFLTAPPMQASSKCNDLTWFKTCWNCEPIGEDERHIKEPLEENFPKWTYNPTVLNPPPT
# LESSQSMSTEPSAYQLFDD]
# end gene g1
###
# start gene g2
Contig41035	AUGUSTUS	gene	10288	15076	0.56	+	.	g2
Contig41035	AUGUSTUS	transcript	10288	15076	0.56	+	.	g2.t1
Contig41035	AUGUSTUS	start_codon	10288	10290	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig41035	AUGUSTUS	intron	10348	10420	0.73	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig41035	AUGUSTUS	intron	10504	11211	0.73	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig41035	AUGUSTUS	intron	11314	11818	0.8	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig41035	AUGUSTUS	intron	12006	14959	0.83	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig41035	AUGUSTUS	CDS	10288	10347	0.82	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig41035	AUGUSTUS	CDS	10421	10503	0.74	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig41035	AUGUSTUS	CDS	11212	11313	0.77	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig41035	AUGUSTUS	CDS	11819	12005	0.86	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig41035	AUGUSTUS	CDS	14960	15076	0.87	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig41035	AUGUSTUS	stop_codon	15074	15076	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggtgatctttccacaacaggaaaataatacaggtcaagaagtgaaactattacgcaagtccccaaacagaaaatgta
# aacaagagttcggcaaatacagacccctggacacaccagaggtgggatcaggtgcctatgaggaaaacaaaacaagagttggcaaacacggaccctgg
# accacaccagaggtggatcaggtgctaggaggagtaagctccctgtgtgaccggtccacatcccactgatcagagccgttgagcacagggagcactgc
# tccacaccgcgtgctggattctgtaaacagacgtcatccatcgcatccaaaagaggaagcgcagtacgtaaagttattaccagtgacggtcattcaaa
# tctctcctcccaaaagcattcctagtgtgaggccagcattcattgattccgcagtcaggaatccagcacgcggtgtggagcagtgctccctgtgctca
# acggctctgatctgtttgtaccggaaccaggagagtatagcaattatcacggacgatgtagccgggcaattaccgtga]
# protein sequence = [MVIFPQQENNTGQEVKLLRKSPNRKCKQEFGKYRPLDTPEVGSGAYEENKTRVGKHGPWTTPEVDQVLGGVSSLCDRS
# TSHXSEPLSTGSTAPHRVLDSVNRRHPSHPKEEAQYVKLLPVTVIQISPPKSIPSVRPAFIDSAVRNPARGVEQCSLCSTALICLYRNQESIAIITDD
# VAGQLP]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093707VN.prfl --predictionStart=0  --predictionEnd=21486  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4103520180911_busco_2432604931_.temp