# 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..117]--> unknown_A (24) <--[0..2]--> unknown_B (20) <--[1..12]--> unknown_C (21) <--[1..8]--> unknown_D (16) <--[1..239]--> unknown_E (28) <--[0..16]--> unknown_F (8) <--[0..23]--> unknown_G (8) <--[0..2]--> unknown_H (25) <--[0..1]--> unknown_I (33) <--[3..5]--> unknown_J (10) <--[6..65]--> unknown_K (24) <--[1..2]--> unknown_L (15) <--[0..28]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6787520180911_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 = 8494, name = Contig67875) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig67875	AUGUSTUS	gene	1	2897	0.18	-	.	g1
Contig67875	AUGUSTUS	transcript	1	2897	0.18	-	.	g1.t1
Contig67875	AUGUSTUS	intron	1	521	0.62	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig67875	AUGUSTUS	intron	660	2307	0.3	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig67875	AUGUSTUS	CDS	522	659	0.47	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig67875	AUGUSTUS	CDS	2308	2897	0.36	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig67875	AUGUSTUS	start_codon	2895	2897	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcaattgaattgtattccaagggtatggttcactgacaaactcacacgtaacattcaacaccgtcaatacgccacta
# gacccaagcatcgtcacacgcgaaacacttatttttatgatgtcctaggcgttccatccagcgccagtcagtctcaaatcaagaatgcctacattgag
# ctgacgaaaaaacatcatccggatgtcagtgaaagtgaagattccagagtgaagtttcagttagtcgctgatgcttacagcgttctggggaacatcca
# ctcccggagaatgtacgaccgagggctggtatccggagcgcgccagcaatctcaaccagaaaaggaggaattcgatccatttgctttaccagtgaaac
# cggttcagactgttttagacaaaattacaatggaaaattacagggcactaacagaaaaaagaatcttacaatcaagtgcgcgagctcgtcaaaggcaa
# caggtggaagaggagaaaattatcaataaacagaaagaactaaaacaaaacaataaggaggtgtatggactgtttatattgctggcagtcgtagcatt
# tggtgtttttggattagaaaatttggttgaatatggccagcggttcttgagaagaagtcgaaaatgtgaaaagttaacagacagacagcagacggaca
# gacagacagacagacgacggacaaaaggcgatcagaatagctcacttgagccttcgctcag]
# protein sequence = [MQLNCIPRVWFTDKLTRNIQHRQYATRPKHRHTRNTYFYDVLGVPSSASQSQIKNAYIELTKKHHPDVSESEDSRVKF
# QLVADAYSVLGNIHSRRMYDRGLVSGARQQSQPEKEEFDPFALPVKPVQTVLDKITMENYRALTEKRILQSSARARQRQQVEEEKIINKQKELKQNNK
# EVYGLFILLAVVAFGVFGLENLVEYGQRFLRRSRKCEKLTDRQQTDRQTDRRRTKGDQNSSLEPSL]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370PYJ.prfl --predictionStart=0  --predictionEnd=27697  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6787520180911_busco_2432604931_.temp