# 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
# --[63..825]--> unknown_A (19) <--[2..191]--> unknown_B (51) <--[0..1]--> unknown_C (47) <--[8..15]--> unknown_D (24) <--[2..13]--> unknown_E (40) <--[0..1]--> unknown_F (16) <--[1..7]--> unknown_G (15) <--[1..23]--> unknown_H (27) <--[9..100]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig777420180911_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 = 2551, name = Contig7774) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig7774	AUGUSTUS	gene	1	2551	0.12	+	.	g1
Contig7774	AUGUSTUS	transcript	1	2551	0.12	+	.	g1.t1
Contig7774	AUGUSTUS	intron	1	47	0.37	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	intron	146	546	0.54	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	intron	669	735	0.96	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	intron	834	1485	0.36	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	intron	1628	1950	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	intron	2040	2311	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	intron	2447	2551	0.93	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	CDS	48	145	0.35	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	CDS	547	668	0.6	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	CDS	736	833	0.36	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	CDS	1486	1627	0.66	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	CDS	1951	2039	1	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig7774	AUGUSTUS	CDS	2312	2446	0.93	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gatggagagagtggacgaaaagttcactatgaagacttttttgatcctccggaagaggagtctgggaaaaaagagaaga
# agtccaaacactccaagagatccagccagaggaggatgagaggtggaggaaaagaagaggaggaggagaaaatgtttgaagaggaagaaatggaagag
# gagatgatgatgaggaggaggaagggaggaggaggaagaagatacgaggtgttgggcagaaaaccacaggaaaaatcaacgtttgagaaacagcaaga
# caaggcgagtagacttgacagagcagagtatcgtgtgggacgcctgagggaaaagatagctaaaatggaggaagccagcctagcagaaaaaccatggc
# aaatgtctggagagataggggccacaaatcgaccggagaacagcttgttggaagaacacttgatgtacgaccagacagtcagactggtaatcctcttt
# gccttgttagcccctgtaataactgaggagacaacacagaccctggaatccatcatcaaacagagaatcaaagacaaggcctttgatgatgtggagag
# gaaagtgaaacctaaagagaatccgatcgagtacaagaaaagggttgttctggaccaggagaagagcaagctcagcctgggggaggtgtatgaacagg
# agtatctcaaacaacag]
# protein sequence = [DGESGRKVHYEDFFDPPEEESGKKEKKSKHSKRSSQRRMRGGGKEEEEEKMFEEEEMEEEMMMRRRKGGGGRRYEVLG
# RKPQEKSTFEKQQDKASRLDRAEYRVGRLREKIAKMEEASLAEKPWQMSGEIGATNRPENSLLEEHLMYDQTVRLVILFALLAPVITEETTQTLESII
# KQRIKDKAFDDVERKVKPKENPIEYKKRVVLDQEKSKLSLGEVYEQEYLKQQ]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370H68.prfl --predictionStart=0  --predictionEnd=21626  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig777420180911_busco_2432604931_.temp