# 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..229]--> unknown_A (15) <--[0..2]--> unknown_B (14) <--[7..9]--> unknown_D (19) <--[0..1]--> unknown_E (39) <--[0..1]--> unknown_F (10) <--[0..9]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2802920180911_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 = 16651, name = Contig28029) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig28029	AUGUSTUS	gene	1	14015	0.01	-	.	g1
Contig28029	AUGUSTUS	transcript	1	14015	0.01	-	.	g1.t1
Contig28029	AUGUSTUS	intron	1	367	0.25	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	intron	378	2556	0.34	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	intron	2720	2981	0.77	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	intron	3107	8125	0.23	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	intron	8403	9566	0.79	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	intron	9624	13299	0.6	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	intron	13480	13865	0.21	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	CDS	368	377	0.33	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	CDS	2557	2719	0.79	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	CDS	2982	3106	0.38	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	CDS	8126	8402	0.54	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	CDS	9567	9623	0.8	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	CDS	13300	13479	0.23	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	CDS	13866	14015	0.28	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig28029	AUGUSTUS	start_codon	14013	14015	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtcggtgttgccaataaaaatcttgaagggtgtttcattatacaaaaatggtacatctgtcgttcatgtgcgcgtgt
# ggttgacttggattgatgtggcattgtatgcgattttactgaccgttgagatcaatttgctgagagtccagaaatatgccttcttcaaaaatccagtt
# ccttcaaaaattccaccagaacttggagggagtaaatttgtgttcgagcatgttaacttcctgtccaaagtcacgttttggtggctaaatggattcct
# agcagatggttacaaaactccttatgaacaggaacatcttgggcaattaccaaaggattatcaggcagagtcagtatataaaagatttaaggctgtgt
# ttgaagatgaattggagaagagcagacggagtggtaagaaactgaacttccacaaggtgtacctgaaggtgttctggaggaacctctgcttggccgga
# gttctgaggcttttcggggacctggtgcagtttgtggggccatggtgcattgaactaatcatcaattacgcctacgtccaggtcaagctgcgagacag
# tgccaatccgaccaatggcagcctgacacagtctccggtttccaatgcttcccaaactgtattcatgtacaactcatcttcagcggtatccatgggtc
# tggtgctgatgtacatgaagatgggctggacggctctgattggtggatctgtggtggttatgtccggtcccattcagtacttcgtcggaaagggcatg
# tctaacatgcagaaaaaagtcatggcgcaatctgataagagagtgaagaaatgtaacgaagcagtccagggcatcaaagttatcaaactcttggcgtg
# ggaatatttctttagacatgacattttagcctccaggaagatggagttgaaacgcctttttgccaacagcattttcagaatacttttcaacgtcgttt
# t]
# protein sequence = [MSVLPIKILKGVSLYKNGTSVVHVRVWLTWIDVALYAILLTVEINLLRVQKYAFFKNPVPSKIPPELGGSKFVFEHVN
# FLSKVTFWWLNGFLADGYKTPYEQEHLGQLPKDYQAESVYKRFKAVFEDELEKSRRSGKKLNFHKVYLKVFWRNLCLAGVLRLFGDLVQFVGPWCIEL
# IINYAYVQVKLRDSANPTNGSLTQSPVSNASQTVFMYNSSSAVSMGLVLMYMKMGWTALIGGSVVVMSGPIQYFVGKGMSNMQKKVMAQSDKRVKKCN
# EAVQGIKVIKLLAWEYFFRHDILASRKMELKRLFANSIFRILFNVV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937128O.prfl --predictionStart=0  --predictionEnd=36423  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2802920180911_busco_2432604931_.temp