# 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
# --[0..69]--> unknown_A (56) <--[0..8]--> unknown_B (98) <--[2..7]--> unknown_C (24) <--[14..125]--> unknown_D (18) <--[0..63]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig116020180911_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 = 23941, name = Contig1160) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig1160	AUGUSTUS	gene	6121	6827	0.7	-	.	g1
Contig1160	AUGUSTUS	transcript	6121	6827	0.7	-	.	g1.t1
Contig1160	AUGUSTUS	stop_codon	6121	6123	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1160	AUGUSTUS	intron	6427	6683	0.74	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1160	AUGUSTUS	CDS	6121	6426	0.85	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1160	AUGUSTUS	CDS	6684	6827	0.79	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1160	AUGUSTUS	start_codon	6825	6827	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgctcaacctcgggggcgcggcaggaagagagggttggcatgagggtataatgaacaatcaacacggttgggcccagc
# tgtcgtggaaaaacatctctcactcgcaggagagacgtgagagttgtcagttctcacgcccacatatcaatcagcaagttgataggagcgtgtattgg
# caggagtataaacgatatgaaggtcacgaggtgcgagtagagctgtattctaaccgcgcaatatggtctcttggagacaaaaatattgtcaataaaga
# tgatagtaccctactagtaattcaacgaatagataaagactacaattggggtcccctaattcgcgccagcccacatatcaacgattatgaccaccatg
# gccggggcgacagaccgatcaaagtgatgaaatattatacggacagattggctaaggacatcaaggacggtagttag]
# protein sequence = [MLNLGGAAGREGWHEGIMNNQHGWAQLSWKNISHSQERRESCQFSRPHINQQVDRSVYWQEYKRYEGHEVRVELYSNR
# AIWSLGDKNIVNKDDSTLLVIQRIDKDYNWGPLIRASPHINDYDHHGRGDRPIKVMKYYTDRLAKDIKDGS]
# end gene g1
###
# start gene g2
Contig1160	AUGUSTUS	gene	11019	12908	0.02	-	.	g2
Contig1160	AUGUSTUS	transcript	11019	12908	0.02	-	.	g2.t1
Contig1160	AUGUSTUS	stop_codon	11019	11021	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig1160	AUGUSTUS	intron	11087	12323	0.49	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig1160	AUGUSTUS	intron	12506	12855	0.12	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig1160	AUGUSTUS	CDS	11019	11086	0.22	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig1160	AUGUSTUS	CDS	12324	12505	0.63	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig1160	AUGUSTUS	CDS	12856	12908	0.12	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig1160	AUGUSTUS	start_codon	12906	12908	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgaaggcatgtcgctcacgacattcgaaacatgcctggggagaacactgcaggtctgtggagtttccgtacggtgaca
# aagaccagagtggtgaattcactctacagatgggggacgtggtcgagttccaggtggcaactgaccgccgtgacaaactgcagagggccaccaaaatc
# cagatctgtcccgagtcattcagccagaactcggagaagagagagaaagtgagtgataatcccgatatgtgctattcacagtttgtcttaatagagac
# gctaagagactctgacgaaatgaggtaa]
# protein sequence = [MKACRSRHSKHAWGEHCRSVEFPYGDKDQSGEFTLQMGDVVEFQVATDRRDKLQRATKIQICPESFSQNSEKREKVSD
# NPDMCYSQFVLIETLRDSDEMR]
# end gene g2
###
# start gene g3
Contig1160	AUGUSTUS	gene	24502	26609	0.2	+	.	g3
Contig1160	AUGUSTUS	transcript	24502	26609	0.2	+	.	g3.t1
Contig1160	AUGUSTUS	start_codon	24502	24504	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig1160	AUGUSTUS	intron	24676	24907	0.98	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig1160	AUGUSTUS	intron	25088	25568	0.98	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig1160	AUGUSTUS	intron	25645	26520	0.41	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig1160	AUGUSTUS	CDS	24502	24675	0.72	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig1160	AUGUSTUS	CDS	24908	25087	0.97	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig1160	AUGUSTUS	CDS	25569	25644	0.72	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig1160	AUGUSTUS	CDS	26521	26609	0.29	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig1160	AUGUSTUS	stop_codon	26607	26609	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgccactagaatggctttttgggcgcaagaagacgccagaggagatgctgaggcagaaccagagagctctaaacaaag
# ccatgcgggacctggatagagagaggtccaaaatggaacaacaggagaaaaaagtcattgctgacataaaaaacatggccaagaaaggacaaatggat
# gcagtgaaggtcatggccaaggatttagtgcggaccaggaggtatgtgaagaagtttatcttaatgagagccaacatccaggcagtgtccttaaagat
# ccagaccctgaaatcaaacaacgcaatggcacaggccatgaaaggggtcactaaagccatgatgaccatgaataaacagatcatggacatgaaggagg
# aaatgatgaatgatgccattgatgatgcaatgggagatgaagacgatgaggaaggagtgatgccaattgtttctcaagttcttgatgagttaggattg
# caactaactgatcaactttcaggtaagttcatgtttgaatatgattaa]
# protein sequence = [MPLEWLFGRKKTPEEMLRQNQRALNKAMRDLDRERSKMEQQEKKVIADIKNMAKKGQMDAVKVMAKDLVRTRRYVKKF
# ILMRANIQAVSLKIQTLKSNNAMAQAMKGVTKAMMTMNKQIMDMKEEMMNDAIDDAMGDEDDEEGVMPIVSQVLDELGLQLTDQLSGKFMFEYD]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093711ZO.prfl --predictionStart=4508  --predictionEnd=45658  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig116020180911_busco_2432604931_.temp