# 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
# --[3..117]--> unknown_A (25) <--[0..1]--> unknown_B (27) <--[0..35]--> unknown_C (11) <--[0..3]--> unknown_D (20) <--[7..15]--> unknown_E (24) <--[8..29]--> unknown_F (20) <--[5..22]--> unknown_G (24) <--[16..63]--> unknown_H (34) <--[0..2]--> unknown_I (43) <--[2..40]--> unknown_J (16) <--[0..1]--> unknown_K (18) <--[11..30]--> unknown_L (48) <--[3..22]--> unknown_M (32) <--[32..332]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig13117320180911_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 = 7406, name = Contig131173) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig131173	AUGUSTUS	gene	270	7406	0.17	-	.	g1
Contig131173	AUGUSTUS	transcript	270	7406	0.17	-	.	g1.t1
Contig131173	AUGUSTUS	stop_codon	270	272	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig131173	AUGUSTUS	intron	442	3506	0.96	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig131173	AUGUSTUS	intron	3550	4707	0.28	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig131173	AUGUSTUS	intron	4853	5358	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig131173	AUGUSTUS	intron	5490	7406	0.67	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig131173	AUGUSTUS	CDS	270	441	0.8	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig131173	AUGUSTUS	CDS	3507	3549	0.4	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig131173	AUGUSTUS	CDS	4708	4852	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig131173	AUGUSTUS	CDS	5359	5489	0.7	-	2	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gagtatatgatgtgattaacaatttgggttccatggctccccgatttgtttttctcccaatagaagagagcggtcgcct
# cttcttctcctgctcttttacccgaggccggagcctaaagcagcagagcaaagactctatagatctagttaccagcgtcctccagcacctcctgaaga
# cagtcactctgattggctgtattatattggtgtttggtcagtcgtatgctttcttggcattagatctttatggaggttcactgctttcctctggggct
# gaggtaaagaaagaaaatatgctaaaggagaaacttatcaggagctgcggtcagcggtcggtcaccgtgcggtcagcggtcggtaccgtttacattgc
# ggtccgggtcgcggttagcgttgcggatccacccggtcagcggttccccaaattgcggtcaccgtcggtcaccgtgcgttctgcgtgcgcgtccaccg
# tgcgttgtggtaaagtttag]
# protein sequence = [VYDVINNLGSMAPRFVFLPIEESGRLFFSCSFTRGRSLKQQSKDSIDLVTSVLQHLLKTVTLIGCIILVFGQSYAFLA
# LDLYGGSLLSSGAEVKKENMLKEKLIRSCGQRSVTVRSAVGTVYIAVRVAVSVADPPGQRFPKLRSPSVTVRSACASTVRCGKV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093707LO.prfl --predictionStart=0  --predictionEnd=25490  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig13117320180911_busco_2432604931_.temp