# 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..83]--> unknown_A (58) <--[3..4]--> unknown_B (15) <--[5..11]--> unknown_C (88) <--[0..1]--> unknown_D (38) <--[10..35]--> unknown_E (13) <--[0..1]--> unknown_F (31) <--[0..38]--> unknown_G (31) <--[0..12]--> unknown_H (27) <--[0..5]--> unknown_I (26) <--[5..21]--> unknown_J (7) <--[0..13]--> unknown_K (17) <--[0..5]--> unknown_L (35) <--[0..42]--> unknown_M (18) <--[0..17]--> unknown_N (15) <--[2..11]--> unknown_O (17) <--[0..2]--> unknown_P (54) <--[0..3]--> unknown_Q (28) <--[0..1]--> unknown_R (68) <--[17..82]--> unknown_S (51) <--[0..29]--> unknown_T (18) <--[1..17]--> unknown_U (23) <--[0..1]--> unknown_V (19) <--[2..16]--> unknown_W (51) <--[1..22]--> unknown_X (29) <--[2..64]--> unknown_Y (32) <--[9..93]--> unknown_AA (13) <--[7..21]--> unknown_AB (17) <--[19..91]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3147320180911_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 = 23074, name = Contig31473) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig31473	AUGUSTUS	gene	6653	6859	0.58	-	.	g1
Contig31473	AUGUSTUS	transcript	6653	6859	0.58	-	.	g1.t1
Contig31473	AUGUSTUS	stop_codon	6653	6655	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig31473	AUGUSTUS	CDS	6653	6859	0.58	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig31473	AUGUSTUS	start_codon	6857	6859	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgacaagaggctcatgggccttaacggtcacctttaattacatgtggaattcggatgagaccggtaaaaccgaggcct
# cgtgtcacagcaggcaggtgtggcacgaaaaagatccttccctgctcaaaggccatgagtgccgagcaaaggccaaaaatgttgcagcccttccccgg
# caatggttggtgacgtctccgtatgagtga]
# protein sequence = [MTRGSWALTVTFNYMWNSDETGKTEASCHSRQVWHEKDPSLLKGHECRAKAKNVAALPRQWLVTSPYE]
# end gene g1
###
# start gene g2
Contig31473	AUGUSTUS	gene	19637	21785	0.38	+	.	g2
Contig31473	AUGUSTUS	transcript	19637	21785	0.38	+	.	g2.t1
Contig31473	AUGUSTUS	start_codon	19637	19639	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig31473	AUGUSTUS	intron	19916	20535	0.98	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig31473	AUGUSTUS	intron	20628	21080	0.94	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig31473	AUGUSTUS	intron	21253	21566	0.99	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig31473	AUGUSTUS	CDS	19637	19915	0.76	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig31473	AUGUSTUS	CDS	20536	20627	0.98	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig31473	AUGUSTUS	CDS	21081	21252	0.93	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig31473	AUGUSTUS	CDS	21567	21785	0.54	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig31473	AUGUSTUS	stop_codon	21783	21785	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggaacccatatcctttccaggaccattttgtgctgacgcatatgatccatcagttgcaatggatacccttgttgacc
# gccgtagaacatctaggctcatcatgctctacaagatctcgtataatcaaatcgacatacatgctcccacttatttaacaccaggggacaacagaaca
# agaggagcccagaagtatctccaactctccgctgacaaggaagtgtatgacaactccttcttcccacgcacaatccttgactggaataatcaaccatc
# gtcagttgttattttacatcacatgttgtccaaggcaactgtcaaagcaaggccaaatgttttatggtgctacaaaaaggaacttgggtttagcagtc
# atcgaaagaagcggatgaagcagttacagaagaagattaagagggggaaactggacatgaaggaggatgatccttttgagctgtttgtggctgccact
# tctatcagatactgttactatgctgagacccacaaaatactgggacagacatttggaatgtgtatattacaggattttgaagccttgactcctaactt
# gctggccagaactatagagactgtagagggagggggcctagtggtgatcctcatcaaaacgatgacttctctaaaacagcttaggtatacagtgtatg
# acaaatggttaagtcaggctaaaacagctgtatacatgacaatggtaagtcaggctaaaacagctatatacaatgacaatggtaagtcaggctaa]
# protein sequence = [MEPISFPGPFCADAYDPSVAMDTLVDRRRTSRLIMLYKISYNQIDIHAPTYLTPGDNRTRGAQKYLQLSADKEVYDNS
# FFPRTILDWNNQPSSVVILHHMLSKATVKARPNVLWCYKKELGFSSHRKKRMKQLQKKIKRGKLDMKEDDPFELFVAATSIRYCYYAETHKILGQTFG
# MCILQDFEALTPNLLARTIETVEGGGLVVILIKTMTSLKQLRYTVYDKWLSQAKTAVYMTMVSQAKTAIYNDNGKSG]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093701V7.prfl --predictionStart=536  --predictionEnd=41722  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3147320180911_busco_2432604931_.temp