# 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
# --[1..169]--> unknown_A (22) <--[3..37]--> unknown_B (28) <--[0..15]--> unknown_C (42) <--[5..29]--> unknown_D (46) <--[45..108]--> unknown_F (53) <--[0..57]--> unknown_G (39) <--[0..117]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2526420180911_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 = 4415, name = Contig25264) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig25264	AUGUSTUS	gene	1482	4415	0.15	-	.	g1
Contig25264	AUGUSTUS	transcript	1482	4415	0.15	-	.	g1.t1
Contig25264	AUGUSTUS	stop_codon	1482	1484	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig25264	AUGUSTUS	intron	1642	2064	0.34	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig25264	AUGUSTUS	intron	2186	2772	0.66	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig25264	AUGUSTUS	intron	2822	4064	0.5	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig25264	AUGUSTUS	intron	4193	4415	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig25264	AUGUSTUS	CDS	1482	1641	0.28	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig25264	AUGUSTUS	CDS	2065	2185	0.6	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig25264	AUGUSTUS	CDS	2773	2821	0.64	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig25264	AUGUSTUS	CDS	4065	4192	0.73	-	2	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gttcaatattgtttcaagatgaaatgaatcattcccagggtgcaacaggaggaggagatgttgttctcaatatggatgg
# tatggataaaaatagatttcagcaacagatgcagctgatcgatcaacaagggatgcttactcctcctctaaaggcacctgaccccacctccacctctg
# gtgatttcatccaggatggagcagacacgatgaagaatatagagaccaccattgtggagttaggaggaatattctcacagctggctcacatggtcaag
# gacaggaaagagattgtacacagaatcgactccaatacagatgatgccgttctaaatgtggaagcggcacacagtgaaattctaaagtattttcaatc
# agtgacatcaaatcgatggcttatgatcaagatatttgctgttctaattttgttcttcattatatttgttgtattcatggcatag]
# protein sequence = [SILFQDEMNHSQGATGGGDVVLNMDGMDKNRFQQQMQLIDQQGMLTPPLKAPDPTSTSGDFIQDGADTMKNIETTIVE
# LGGIFSQLAHMVKDRKEIVHRIDSNTDDAVLNVEAAHSEILKYFQSVTSNRWLMIKIFAVLILFFIIFVVFMA]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370U71.prfl --predictionStart=0  --predictionEnd=22183  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2526420180911_busco_2432604931_.temp