# 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
# --[10..101]--> unknown_B (15) <--[0..1]--> unknown_C (14) <--[10..34]--> unknown_E (71) <--[0..24]--> unknown_F (24) <--[0..1]--> unknown_G (25) <--[11..61]--> unknown_H (63) <--[1..2]--> unknown_I (22) <--[13..37]--> unknown_J (17) <--[2..14]--> unknown_K (31) <--[0..1]--> unknown_L (9) <--[1..4]--> unknown_M (10) <--[0..12]--> unknown_N (16) <--[0..4]--> unknown_O (11) <--[3..49]--> unknown_P (17) <--[1..15]--> unknown_Q (68) <--[8..39]--> unknown_S (27) <--[18..46]--> unknown_U (38) <--[3..20]--> unknown_V (9) <--[0..1]--> unknown_W (23) <--[11..97]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5838420180911_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 = 5259, name = Contig58384) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig58384	AUGUSTUS	gene	23	3804	0.35	-	.	g1
Contig58384	AUGUSTUS	transcript	23	3804	0.35	-	.	g1.t1
Contig58384	AUGUSTUS	stop_codon	23	25	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig58384	AUGUSTUS	intron	109	1101	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig58384	AUGUSTUS	intron	1307	2477	0.83	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig58384	AUGUSTUS	intron	2556	3702	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig58384	AUGUSTUS	CDS	23	108	0.86	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig58384	AUGUSTUS	CDS	1102	1306	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig58384	AUGUSTUS	CDS	2478	2555	0.98	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig58384	AUGUSTUS	CDS	3703	3804	0.51	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig58384	AUGUSTUS	start_codon	3802	3804	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggagggaattaatattgtgttgaagagtttatatgacgtgtgtcttcagaccgtggaaccacaggggggagaactgt
# ggtctgatgatgtctacaaactggcggcagtacatagtacggagggagtactgggctatatctactgtgacttgttcgacagaccaggcaagcacatg
# atggactgtcactgtacgattcgtggagggagggaagaggaggacggggggtaccagctccctgtggtggttttgaactgtaacttagctcgtcccca
# caccaacgcccccactctactgacccctggcctcatgagaaatctttttcatgaatttggacatgccatgcactccatgcttggaagaacaaagtatc
# agcatgtgacaggtacaaggtgccccacagattttgcagaggttccttcagaatttatggagttctttgccacagatccaagggtaagcaaattttaa]
# protein sequence = [MEGINIVLKSLYDVCLQTVEPQGGELWSDDVYKLAAVHSTEGVLGYIYCDLFDRPGKHMMDCHCTIRGGREEEDGGYQ
# LPVVVLNCNLARPHTNAPTLLTPGLMRNLFHEFGHAMHSMLGRTKYQHVTGTRCPTDFAEVPSEFMEFFATDPRVSKF]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093705E5.prfl --predictionStart=0  --predictionEnd=21309  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5838420180911_busco_2432604931_.temp