# 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..16]--> unknown_A (12) <--[0..3]--> unknown_B (17) <--[1..4]--> unknown_C (33) <--[10..16]--> unknown_E (45) <--[1..20]--> unknown_F (66) <--[0..2]--> unknown_G (13) <--[3..11]--> unknown_H (23) <--[10..57]--> unknown_I (61) <--[0..2]--> unknown_J (14) <--[0..5]--> unknown_K (26) <--[0..15]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig8411220180911_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 = 12718, name = Contig84112) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig84112	AUGUSTUS	gene	1	6989	0.33	+	.	g1
Contig84112	AUGUSTUS	transcript	1	6989	0.33	+	.	g1.t1
Contig84112	AUGUSTUS	intron	1	201	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	intron	408	1312	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	intron	1408	2072	0.96	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	intron	2255	2581	0.44	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	intron	2719	6473	0.62	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	intron	6643	6800	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	CDS	202	407	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	CDS	1313	1407	1	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	CDS	2073	2254	0.94	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	CDS	2582	2718	0.38	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	CDS	6474	6642	0.79	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	CDS	6801	6989	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig84112	AUGUSTUS	stop_codon	6987	6989	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gttcatggaggagattttccccatctgatggtgtatggaccatcaggagcaggtaagaagactcgcatcatgtgtctgc
# tgagggaactgtatggatcaggagtggaaaaactacgtattgagcaaaacaatttcactacaccttccaacaaaaagatcgaaatctcaaccatctcc
# agcaattaccacattgaagtcaatccaagcgatgtcggaatccaagacagggttgttattcaagaattaatcaaaacagtagcgcaaacaaacaactt
# ggattcctcacaaagagacttcaaagttgtcatcctcaccgaagtagataaactaacaaaggatgcacagcatgctcttcgtcgcacaatggagaaat
# acatggcaacttgcaggctgattctgtgttgtatatcaacaagtaaagtcattccagccatccgcagtcgatgtctcgggatcagggtttcagcacct
# accattgaccagatgacacagattctgcagacagtttgtaagaaggaaggatgtccaatacctatagagttagctaaaagagtggccgagaaaagcaa
# acggaatctcaggagagcattgctcatggcagaagcttgtaaagttcaacagactccattaaagtcagatcaagaggtttccgagccagactgggaag
# tgtatctcaaggaaacagctaacatgattatccaacagcaatcaccacggcgactgctggaggtcagaggtcgtttatatgaactcctgacccactgt
# ataccagcagaaatcatcatgaagggattgttacaagaattggtgataaactgtgatggtgaactgaaaactgaggtggtacaatctgcagcattttt
# tcaacatcgactccaactcgggcagaaggctatctatcatttggaggcctttgtggcaaagtttatggccatctacaaaagattcatggaagaaagca
# ttgcggatctcttctaa]
# protein sequence = [VHGGDFPHLMVYGPSGAGKKTRIMCLLRELYGSGVEKLRIEQNNFTTPSNKKIEISTISSNYHIEVNPSDVGIQDRVV
# IQELIKTVAQTNNLDSSQRDFKVVILTEVDKLTKDAQHALRRTMEKYMATCRLILCCISTSKVIPAIRSRCLGIRVSAPTIDQMTQILQTVCKKEGCP
# IPIELAKRVAEKSKRNLRRALLMAEACKVQQTPLKSDQEVSEPDWEVYLKETANMIIQQQSPRRLLEVRGRLYELLTHCIPAEIIMKGLLQELVINCD
# GELKTEVVQSAAFFQHRLQLGQKAIYHLEAFVAKFMAIYKRFMEESIADLF]
# end gene g1
###
# start gene g2
Contig84112	AUGUSTUS	gene	11374	12718	0.96	-	.	g2
Contig84112	AUGUSTUS	transcript	11374	12718	0.96	-	.	g2.t1
Contig84112	AUGUSTUS	stop_codon	11374	11376	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig84112	AUGUSTUS	intron	11856	11981	1	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig84112	AUGUSTUS	intron	12150	12454	0.99	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig84112	AUGUSTUS	intron	12615	12718	0.98	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig84112	AUGUSTUS	CDS	11374	11855	0.99	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig84112	AUGUSTUS	CDS	11982	12149	1	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig84112	AUGUSTUS	CDS	12455	12614	0.98	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [catcctgaggcgcagtacttcctgggaatctgctatgagcagggctggggggtagaggttaatgagtgcaaggcagccc
# atctgtactcacaagcagcccagtctgggcacgacggagccctgtataatctagctgtttttcatgaacacggaattggaggattacctgaagataaa
# atatctgcggaggagctatacagaaaatcagcaaaccttggtaatgaaatggcaggagataaagtgatggaaattgatgccaagagggtggtcaagcc
# atggaaagggaactatccaagctgtaaaatggacgaattcctgtatgatatagaccagttcagtaatagccaaaatgacagtgccagcatacctccag
# gaaaagatgacaaaaggtttatacctcaaagtgaactgagaacagatataaagggaaataactccaggatctcgctccccttgtcttcctcctctccg
# tctctaactgagtacgttcgccagcacacctcacagctacagattggggcggttcctgactccggccttcttccactacttaccactcacgggtcggg
# agaagcgtggtatcctcagttcgggagccctagagtcgcctcccctgtctctccctcagtgctgttcacactgggagatgaggaggaggagctgatgg
# ctgttaacagattaaacctcgctgtcagtcagacggacatacagttccacgtcccggaaaagagccatcaccatttctgctccatgatacagaggaac
# tccaccatgcctgatctgcagagtcaggcagtgtcctgcgtttga]
# protein sequence = [HPEAQYFLGICYEQGWGVEVNECKAAHLYSQAAQSGHDGALYNLAVFHEHGIGGLPEDKISAEELYRKSANLGNEMAG
# DKVMEIDAKRVVKPWKGNYPSCKMDEFLYDIDQFSNSQNDSASIPPGKDDKRFIPQSELRTDIKGNNSRISLPLSSSSPSLTEYVRQHTSQLQIGAVP
# DSGLLPLLTTHGSGEAWYPQFGSPRVASPVSPSVLFTLGDEEEELMAVNRLNLAVSQTDIQFHVPEKSHHHFCSMIQRNSTMPDLQSQAVSCV]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093705DM.prfl --predictionStart=0  --predictionEnd=26953  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig8411220180911_busco_2432604931_.temp