# 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
# --[41..494]--> unknown_E (61) <--[0..1]--> unknown_F (19) <--[7..22]--> unknown_G (44) <--[0..2]--> unknown_H (22) <--[5..26]--> unknown_I (34) <--[2..5]--> unknown_J (39) <--[0..82]--> unknown_K (39) <--[17..54]--> unknown_M (29) <--[1..18]--> unknown_N (33) <--[0..1]--> unknown_O (21) <--[11..76]--> unknown_P (32) <--[23..51]--> unknown_R (19) <--[0..1]--> unknown_S (10) <--[21..47]--> unknown_U (15) <--[0..2]--> unknown_V (28) <--[4..11]--> unknown_W (21) <--[5..18]--> unknown_X (20) <--[11..35]--> unknown_Y (17) <--[0..498]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig126820180911_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 = 12496, name = Contig1268) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig1268	AUGUSTUS	gene	1	11266	0.03	-	.	g1
Contig1268	AUGUSTUS	transcript	1	11266	0.03	-	.	g1.t1
Contig1268	AUGUSTUS	intron	1	520	0.52	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	intron	584	1037	0.6	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	intron	1258	2150	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	intron	2237	2739	0.48	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	intron	2780	4627	0.22	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	intron	4682	4878	0.24	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	intron	4885	6816	0.26	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	intron	6830	7262	0.5	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	intron	7336	7775	0.84	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	intron	7891	8070	0.92	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	intron	8154	11155	0.5	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	CDS	521	583	0.58	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	CDS	1038	1257	0.98	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	CDS	2151	2236	0.92	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	CDS	2740	2779	0.51	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	CDS	4628	4681	0.37	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	CDS	4879	4884	0.36	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	CDS	6817	6829	0.49	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	CDS	7263	7335	0.95	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	CDS	7776	7890	0.92	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	CDS	8071	8153	0.92	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	CDS	11156	11266	0.65	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig1268	AUGUSTUS	start_codon	11264	11266	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcggcgtccaggagtgatgccacgtccctctcaacctttgatggggttgaaaaccttgtaaacatgaccgatattc
# agaaggcttacgatgaattaagtaaagaagaggaggatatgaacacagagctagacaatctcttggaacatcaatcatcactcgagaacaagatgagt
# ggtcttcataagattttgcctaatctgcagattcttgagacagattctaaacagctttccagtatggtctcctttacgtctaccctcgctgaaaatgt
# cagcagtaaagtgcggcagttagatgtggctaaagctgcaggtcatgttcacagatttaggagtttagatgaaaacattttaagaatgtcagaagaat
# cagatgaaggttatagtcacaggttcaggttcagacaagtcacagaatgctgtctttcaccggtcctaaatgcacctgaaaaggtgatatggaattgg
# cttatagtaatgacactcttaagggctgtttccatggatacagtagacatgacctcatatacatccagtatggtggatgactcattttatattgtaaa
# gaagtgtgtcaggagagctgtatcgagttccagtgtggacgggctttgtgcaatgttaaaccatgctagtactgtgctagagcaggacttccgggaag
# tgttgttctcgcgagtgagggccggttttccgtcaggcttcgatctctcccaggcctataacatggtgcagtccagcatacagcagggaaaattacag
# agtgctgatcaggagaaagccaagacaacatttctggcagccatgaataatgcagaaatcagttgtgaatattgcaaatccttgaaatccaatataga
# g]
# protein sequence = [MAASRSDATSLSTFDGVENLVNMTDIQKAYDELSKEEEDMNTELDNLLEHQSSLENKMSGLHKILPNLQILETDSKQL
# SSMVSFTSTLAENVSSKVRQLDVAKAAGHVHRFRSLDENILRMSEESDEGYSHRFRFRQVTECCLSPVLNAPEKVIWNWLIVMTLLRAVSMDTVDMTS
# YTSSMVDDSFYIVKKCVRRAVSSSSVDGLCAMLNHASTVLEQDFREVLFSRVRAGFPSGFDLSQAYNMVQSSIQQGKLQSADQEKAKTTFLAAMNNAE
# ISCEYCKSLKSNIE]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093706RN.prfl --predictionStart=0  --predictionEnd=27531  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig126820180911_busco_2432604931_.temp