# 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..82]--> unknown_A (29) <--[14..69]--> unknown_C (14) <--[4..27]--> unknown_D (27) <--[0..9]--> unknown_E (26) <--[3..57]--> unknown_F (26) <--[22..129]--> unknown_G (14) <--[0..1]--> unknown_H (22) <--[0..25]--> unknown_I (19) <--[28..180]--> unknown_L (43) <--[0..1]--> unknown_M (33) <--[8..14]--> unknown_O (11) <--[4..7]--> unknown_P (23) <--[10..56]--> unknown_R (24) <--[0..16]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig8765820180911_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 = 7465, name = Contig87658) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig87658	AUGUSTUS	gene	1544	6972	0.04	-	.	g1
Contig87658	AUGUSTUS	transcript	1544	6972	0.04	-	.	g1.t1
Contig87658	AUGUSTUS	stop_codon	1544	1546	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig87658	AUGUSTUS	intron	1685	2369	0.17	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87658	AUGUSTUS	intron	2441	3906	0.09	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87658	AUGUSTUS	intron	4111	4708	0.87	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87658	AUGUSTUS	intron	4971	6825	0.54	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87658	AUGUSTUS	CDS	1544	1684	0.44	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig87658	AUGUSTUS	CDS	2370	2440	0.16	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig87658	AUGUSTUS	CDS	3907	4110	0.67	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig87658	AUGUSTUS	CDS	4709	4970	0.94	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig87658	AUGUSTUS	CDS	6826	6972	0.47	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig87658	AUGUSTUS	start_codon	6970	6972	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgactcgaagacaacacgatgtttgccgattccttttgtttcagcactttgggaagcaggcgtctgttgttggaaaat
# atctactacagaaatctttgtgtcctcttcaattaatagcaacagagctaaatatagaaaccgagcaggtgaagaagattttgtgcattctaattcaa
# caaaacatagtgacatttgaacagcacaaaaagggttttattgaatattcaatcaagaaggaggagatattaaaccggttatggtttcctaagtttat
# ttactgtgccaagactttgtatggagatgcagccgaacttttactggaagaaatcttgcagagagggcaagttcaaatgtctaaagtcgtggaggtgg
# tgatgcagagatttaatgaggcactagaaacttcaggaaaaccaaaaatttcagagagctttgtgtctgaaaagttttctaacttagtgaagactcac
# tttctacaaagatgtatggatccagtgaaatctgcctccaataaagtgataggtctggatatatcggctcaggaggagtccttgtacagatttaccga
# ggtaggtctagagatgacagctcaccttgtacaggatgtaccagatctgtctaggaagaggaaaaagtcacatgataatggtccaccagccaaaagat
# caaagttggaggaagggggcccagacgatgaggaggacgatggaatcttttggagagtccactgtgacagatttcgtcaacactttcgcgaccaagct
# atagtgcaggccgtttctaacaagattgatagggtgagtcaccagtggggtcctgtatag]
# protein sequence = [MTRRQHDVCRFLLFQHFGKQASVVGKYLLQKSLCPLQLIATELNIETEQVKKILCILIQQNIVTFEQHKKGFIEYSIK
# KEEILNRLWFPKFIYCAKTLYGDAAELLLEEILQRGQVQMSKVVEVVMQRFNEALETSGKPKISESFVSEKFSNLVKTHFLQRCMDPVKSASNKVIGL
# DISAQEESLYRFTEVGLEMTAHLVQDVPDLSRKRKKSHDNGPPAKRSKLEEGGPDDEEDDGIFWRVHCDRFRQHFRDQAIVQAVSNKIDRVSHQWGPV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370C5A.prfl --predictionStart=0  --predictionEnd=24985  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig8765820180911_busco_2432604931_.temp