# 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
# --[9..505]--> unknown_B (38) <--[4..24]--> unknown_C (67) <--[0..1]--> unknown_D (6) <--[0..1]--> unknown_E (24) <--[1..9]--> unknown_F (67) <--[6..108]--> unknown_G (31) <--[4..7]--> unknown_H (38) <--[1..5]--> unknown_I (16) <--[0..1]--> unknown_J (56) <--[8..14]--> unknown_K (58) <--[0..297]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig1995720180911_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 = 23326, name = Contig19957) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig19957	AUGUSTUS	gene	285	23326	0.01	-	.	g1
Contig19957	AUGUSTUS	transcript	285	23326	0.01	-	.	g1.t1
Contig19957	AUGUSTUS	exon	285	932	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig19957	AUGUSTUS	exon	1974	3036	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig19957	AUGUSTUS	exon	3236	3865	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig19957	AUGUSTUS	exon	6655	6824	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig19957	AUGUSTUS	exon	8841	8894	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig19957	AUGUSTUS	exon	10912	11158	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig19957	AUGUSTUS	stop_codon	10977	10979	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig19957	AUGUSTUS	intron	11159	23326	0.03	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig19957	AUGUSTUS	CDS	10977	11158	0.36	-	2	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [cgactacagcacaggcgctggacgtgaacgacgaactttttccgaggatgttccgtacaaaggaactgaggaactcact
# cgctagcatctgcagtctccattcgggctggtacaaaagtcccgccttcaaaccaatactgagaagatccactttggaacctacaaaaggaccagcag
# gatag]
# protein sequence = [TTAQALDVNDELFPRMFRTKELRNSLASICSLHSGWYKSPAFKPILRRSTLEPTKGPAG]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370P9T.prfl --predictionStart=0  --predictionEnd=23326  --species=fly ./tmp/Contig1995720180911_busco_2432604931_.temp