# 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
# --[8..201]--> unknown_A (16) <--[0..7]--> unknown_B (33) <--[0..3]--> unknown_C (45) <--[0..1]--> unknown_D (15) <--[7..8]--> unknown_F (12) <--[0..1]--> unknown_G (22) <--[3..13]--> unknown_H (38) <--[3..25]--> unknown_I (24) <--[1..5]--> unknown_J (16) <--[9..25]--> unknown_L (29) <--[0..71]--> unknown_M (20) <--[0..1]--> unknown_N (13) <--[12..47]--> unknown_P (23) <--[5..7]--> unknown_Q (21) <--[12..70]--> unknown_T (22) <--[0..160]--> unknown_U (34) <--[0..2]--> unknown_V (8) <--[0..6]--> unknown_W (25) <--[1..3]--> unknown_X (29) <--[0..37]--> unknown_Y (15) <--[9..49]--> unknown_AA (23) <--[3..25]--> unknown_AB (10) <--[4..6]--> unknown_AC (12) <--[37..595]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig457020180911_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 = 8594, name = Contig4570) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig4570	AUGUSTUS	gene	1	8594	0.05	+	.	g1
Contig4570	AUGUSTUS	transcript	1	8594	0.05	+	.	g1.t1
Contig4570	AUGUSTUS	intron	1	537	0.67	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig4570	AUGUSTUS	intron	726	3519	0.41	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig4570	AUGUSTUS	intron	3533	7486	0.33	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig4570	AUGUSTUS	intron	7513	7757	0.25	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig4570	AUGUSTUS	intron	7874	8297	0.24	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig4570	AUGUSTUS	intron	8418	8594	0.52	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig4570	AUGUSTUS	CDS	538	725	0.72	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig4570	AUGUSTUS	CDS	3520	3532	0.51	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig4570	AUGUSTUS	CDS	7487	7512	0.28	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig4570	AUGUSTUS	CDS	7758	7873	0.25	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig4570	AUGUSTUS	CDS	8298	8417	0.51	+	1	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gtgatgacgtccattttgttgttttgcataccagaaagctggatgatgagatacgagcagtagtgaggggacagaccaa
# tgctggggaggatggaaggctggccctggaagaagcacagagggcaatacaagagctgttctctaagattaaggaaatcaaagaaaaggcagacaaat
# ccgaagaaatgggagctggagaaggtgtaaagcatgttaaataccggtatgttaaagaaataacaagggacatcaagcaactggatcatgcaaagaag
# aatttgaccagctcaattacaacattaaatcatctacacatgttagtgggaggagtcgattcactctcgactatggctaagaaaagacaatatgggga
# agtagcaaatttacttcaaggagttcaaaatgtgttggaacactttcaaaaatacatggaaattccacaaataaagcagctagcggacag]
# protein sequence = [DDVHFVVLHTRKLDDEIRAVVRGQTNAGEDGRLALEEAQRAIQELFSKIKEIKEKADKSEEMGAGEGVKHVKYRYVKE
# ITRDIKQLDHAKKNLTSSITTLNHLHMLVGGVDSLSTMAKKRQYGEVANLLQGVQNVLEHFQKYMEIPQIKQLAD]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937092W.prfl --predictionStart=0  --predictionEnd=28421  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig457020180911_busco_2432604931_.temp