# 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
# --[4..158]--> unknown_A (31) <--[0..4]--> unknown_B (26) <--[2..19]--> unknown_C (21) <--[1..5]--> unknown_D (21) <--[0..1]--> unknown_E (30) <--[1..4]--> unknown_F (34) <--[2..70]--> unknown_G (19) <--[0..1]--> unknown_H (8) <--[2..6]--> unknown_I (14) <--[1..18]--> unknown_J (11) <--[20..292]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5580120180911_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 = 18273, name = Contig55801) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig55801	AUGUSTUS	gene	6468	10602	0.33	+	.	g1
Contig55801	AUGUSTUS	transcript	6468	10602	0.33	+	.	g1.t1
Contig55801	AUGUSTUS	start_codon	6468	6470	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig55801	AUGUSTUS	intron	7203	10482	0.86	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig55801	AUGUSTUS	CDS	6468	7202	0.33	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig55801	AUGUSTUS	CDS	10483	10602	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig55801	AUGUSTUS	stop_codon	10600	10602	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgatggacttactggtagtagaagaaattttgcaaaaagcattgcaaaatgatcacgaaacgataaacctaagccatc
# gaaacattgctgtcctctcaagcagctttcaaaaacttaaacacgtcaaacgtttgttactgaacgacaatcagatcatggtccctccatctgagatc
# actgacctaatcaaactggaggaacttgttctgaataacaacaaactgacattactgccaacgggactgtgcaaacttacaaatctgacgtaccttaa
# tttgtgtcataatccactgagtgttctctccgacgagatttgtcaactaagcagtcttcatcagctgtggattgtcgattgtcaactagttaacctgc
# catcgaacattggaaacttaaaatatctaaggaaattaagtgtgcgtgagaactatctagagtctcttcctcccagttttgtagaactagaaaatcta
# tcttggttgtgcttatcagaaaataccttgagatgtttaccaaaatcttttcataaattgaaaagcttgactcatttgaatttgaaccagaatgaaat
# gactcatattccagagtcgatttcagaactacccaatttaatttgtttgttgatgaagagtaatttcatcaaagaagtaaaagatgacacaatactgg
# ccttatccaaactgaccaagtttgatctcagagataatgaaatccaagtaaaaccaccgcactggaagagcactgacgaacttacgagtggccttgat
# gaaattgatgatgactgctcagaggaggatgaagatgatgagtgtgaagatggtgatgacagtgataatgactgccaaaaggataactga]
# protein sequence = [MMDLLVVEEILQKALQNDHETINLSHRNIAVLSSSFQKLKHVKRLLLNDNQIMVPPSEITDLIKLEELVLNNNKLTLL
# PTGLCKLTNLTYLNLCHNPLSVLSDEICQLSSLHQLWIVDCQLVNLPSNIGNLKYLRKLSVRENYLESLPPSFVELENLSWLCLSENTLRCLPKSFHK
# LKSLTHLNLNQNEMTHIPESISELPNLICLLMKSNFIKEVKDDTILALSKLTKFDLRDNEIQVKPPHWKSTDELTSGLDEIDDDCSEEDEDDECEDGD
# DSDNDCQKDN]
# end gene g1
###
# start gene g2
Contig55801	AUGUSTUS	gene	11969	18166	0.17	-	.	g2
Contig55801	AUGUSTUS	transcript	11969	18166	0.17	-	.	g2.t1
Contig55801	AUGUSTUS	stop_codon	11969	11971	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	intron	12102	14831	0.68	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	intron	14956	15290	0.79	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	intron	15379	15851	0.67	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	intron	16078	16239	0.4	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	intron	16274	17982	0.4	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	CDS	11969	12101	0.85	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	CDS	14832	14955	0.68	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	CDS	15291	15378	0.67	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	CDS	15852	16077	1	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	CDS	16240	16273	0.4	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	CDS	17983	18166	0.4	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig55801	AUGUSTUS	start_codon	18164	18166	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgtcacaatgcaatgggcagatgctaacacagcatggactgaaaacgtttatcgcagcatgggtggaagcatttagtt
# tgctgatttcggttgagattcagctcggctggatatttggactggaccctggtgccttcaccaagtccagatatcctgccgagccgaatctcaacgag
# atgattatgaccacaaaaaaaaagatatttttccaggtagggacaaaatacaacttgaacgcaatatcacacgactgtgcaatacggctggtacagag
# ggcgctggacctgggcgccaacattgcagaggtctatgtcgacacagtaggggacccagaaaaataccagaccaagttaaagaacctgtttcccaaca
# ttcagatcacagtagccaagaaggctgatgctctctatcccatcgtcagtgcagccagtatatgtgcgaaggtttgtagagaccgagcattgtctaag
# tggaaattccaagaggagataactgttgatgaggaggggtatggtagtggttaccccggagatccgaagacgaaaaagtttttgtcagacagcatgga
# caaggtgttcggctttccccagtttgtccgctttggttggtccactgccgctgtgattttacagaaaaatgctgtgcaggttaaatgggatgatgagg
# aggaagaagaaaaggatacagtcaagttaacatcattttttcaaaagaaaggtcatgaccccaaacttgagagacactcgtattttaaagacagatgt
# cttggctctgtagaatcattttaa]
# protein sequence = [MSQCNGQMLTQHGLKTFIAAWVEAFSLLISVEIQLGWIFGLDPGAFTKSRYPAEPNLNEMIMTTKKKIFFQVGTKYNL
# NAISHDCAIRLVQRALDLGANIAEVYVDTVGDPEKYQTKLKNLFPNIQITVAKKADALYPIVSAASICAKVCRDRALSKWKFQEEITVDEEGYGSGYP
# GDPKTKKFLSDSMDKVFGFPQFVRFGWSTAAVILQKNAVQVKWDDEEEEEKDTVKLTSFFQKKGHDPKLERHSYFKDRCLGSVESF]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370JIK.prfl --predictionStart=0  --predictionEnd=36073  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5580120180911_busco_2432604931_.temp