# 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
# --[56..347]--> unknown_B (43) <--[4..77]--> unknown_C (18) <--[21..106]--> unknown_F (18) <--[0..1]--> unknown_G (18) <--[3..35]--> unknown_H (18) <--[0..2]--> unknown_I (15) <--[0..14]--> unknown_J (22) <--[33..62]--> unknown_N (11) <--[1..20]--> unknown_O (13) <--[2..7]--> unknown_P (22) <--[1..24]--> unknown_Q (25) <--[11..49]--> unknown_S (12) <--[6..33]--> unknown_U (15) <--[1..11]--> unknown_V (14) <--[7..30]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6320220180911_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 = 5870, name = Contig63202) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig63202	AUGUSTUS	gene	1075	4317	0.32	+	.	g1
Contig63202	AUGUSTUS	transcript	1075	4317	0.32	+	.	g1.t1
Contig63202	AUGUSTUS	start_codon	1075	1077	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig63202	AUGUSTUS	intron	1114	2866	0.88	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig63202	AUGUSTUS	intron	3023	3371	0.99	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig63202	AUGUSTUS	intron	3435	3530	0.68	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig63202	AUGUSTUS	intron	3580	4186	0.45	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig63202	AUGUSTUS	CDS	1075	1113	0.78	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig63202	AUGUSTUS	CDS	2867	3022	0.88	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig63202	AUGUSTUS	CDS	3372	3434	0.92	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig63202	AUGUSTUS	CDS	3531	3579	0.46	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig63202	AUGUSTUS	CDS	4187	4317	0.45	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig63202	AUGUSTUS	stop_codon	4315	4317	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtttatgataggatggtgttctaggtatgataggatggaggaggtgactctagtgggtaggatttgctgtgatagtc
# tgggtaagctgaatgctaagtcggtgattctggagggatctcgggacacgtccgccggccgctacattcctctagatctaagtgacctcaaacagtac
# tcactgtttccagggcagatcgtggcaatggatggaacaaatacttctggacagaaatttgtggtgaaaaagctatatgagggtgttgtacaaccatt
# gccagcatgttcaaatgagaaggatgaaattgagttgcctgagatgacagttttgattgctgctggacccttctcaacatcagacaacttgtcttttg
# agccactctcagatctagtgaaattcatcagaaaagataaaccagatattgtgatattggtatag]
# protein sequence = [MFMIGWCSRYDRMEEVTLVGRICCDSLGKLNAKSVILEGSRDTSAGRYIPLDLSDLKQYSLFPGQIVAMDGTNTSGQK
# FVVKKLYEGVVQPLPACSNEKDEIELPEMTVLIAAGPFSTSDNLSFEPLSDLVKFIRKDKPDIVILV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370L77.prfl --predictionStart=0  --predictionEnd=24308  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6320220180911_busco_2432604931_.temp