# 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..317]--> unknown_A (10) <--[0..15]--> unknown_B (32) <--[4..9]--> unknown_C (111) <--[0..51]--> unknown_D (52) <--[2..14]--> unknown_E (40) <--[0..2]--> unknown_F (69) <--[2..39]--> unknown_G (23) <--[0..45]--> unknown_H (20) <--[0..4]--> unknown_I (68) <--[0..4]--> unknown_J (12) <--[0..19]--> unknown_K (15) <--[0..1]--> unknown_L (15) <--[0..2]--> unknown_M (12) <--[0..7]--> unknown_N (29) <--[0..20]--> unknown_O (15) <--[17..63]--> unknown_Q (43) <--[0..117]--> unknown_R (32) <--[19..383]--> unknown_S (29) <--[35..83]--> unknown_U (19) <--[0..1]--> unknown_V (15) <--[7..55]--> unknown_W (13) <--[10..19]--> unknown_Y (13) <--[1..15]--> unknown_Z (17) <--[0..50]--> unknown_AA (16) <--[0..1]--> unknown_AB (36) <--[0..40]--> unknown_AC (26) <--[5..7]--> unknown_AD (11) <--[1..12]--> unknown_AE (26) <--[2..13]--> unknown_AF (21) <--[16..182]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4335020180911_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 = 6625, name = Contig43350) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig43350	AUGUSTUS	gene	1	634	0.53	+	.	g1
Contig43350	AUGUSTUS	transcript	1	634	0.53	+	.	g1.t1
Contig43350	AUGUSTUS	intron	1	487	0.53	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig43350	AUGUSTUS	CDS	488	634	0.53	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig43350	AUGUSTUS	stop_codon	632	634	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gaagtgaagagatcagcaggtagctcggggttcatgggcagtaactctgatgctccgcacgcagctagctgtatacagt
# tcctgacggaagagaccgcgggggcggggctgccgaatcgtgcactggacccattcatcgcagactga]
# protein sequence = [EVKRSAGSSGFMGSNSDAPHAASCIQFLTEETAGAGLPNRALDPFIAD]
# end gene g1
###
# start gene g2
Contig43350	AUGUSTUS	gene	903	5150	0.49	-	.	g2
Contig43350	AUGUSTUS	transcript	903	5150	0.49	-	.	g2.t1
Contig43350	AUGUSTUS	stop_codon	903	905	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig43350	AUGUSTUS	intron	1080	3267	0.91	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig43350	AUGUSTUS	intron	3422	5124	0.73	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig43350	AUGUSTUS	CDS	903	1079	0.81	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig43350	AUGUSTUS	CDS	3268	3421	0.74	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig43350	AUGUSTUS	CDS	5125	5150	0.91	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig43350	AUGUSTUS	start_codon	5148	5150	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggagaaatctgggtcttcaacaagagctgcacacaataattcctctgtccgtgtactgaccttgcagacgctggatg
# gggagtcccgtctatctatggtgtacgactgctcgaatgccaggattatcatccgaaccttcaggcattgctcaactgcaaagagaattccagaacta
# gagagctacacacaatacattcctctgtccgtgtacgaccttcagacctggatggggagtccgtctatctatgtgtacgactgctcgaatgccggaat
# tatcatcgaactcttcaggcaattctcactgcaaagagaatcagaactagaggtaaagaaacagaaagccgtaggcttctaa]
# protein sequence = [MEKSGSSTRAAHNNSSVRVLTLQTLDGESRLSMVYDCSNARIIIRTFRHCSTAKRIPELESYTQYIPLSVYDLQTWMG
# SPSIYVYDCSNAGIIIELFRQFSLQRESELEVKKQKAVGF]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093700N7.prfl --predictionStart=0  --predictionEnd=25193  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4335020180911_busco_2432604931_.temp