# 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..117]--> unknown_A (9) <--[0..2]--> unknown_B (13) <--[0..7]--> unknown_C (107) <--[0..2]--> unknown_D (9) <--[0..1]--> unknown_E (21) <--[0..9]--> unknown_F (70) <--[0..307]--> unknown_G (29) <--[0..59]--> unknown_H (25) <--[23..87]--> unknown_K (21) <--[2..25]--> unknown_L (28) <--[0..197]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig9857520180911_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 = 4739, name = Contig98575) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig98575	AUGUSTUS	gene	1	4739	0.64	+	.	g1
Contig98575	AUGUSTUS	transcript	1	4739	0.64	+	.	g1.t1
Contig98575	AUGUSTUS	intron	1	543	0.75	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig98575	AUGUSTUS	intron	619	2748	0.94	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig98575	AUGUSTUS	intron	2892	3008	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig98575	AUGUSTUS	intron	3200	4603	0.85	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig98575	AUGUSTUS	CDS	544	618	0.94	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig98575	AUGUSTUS	CDS	2749	2891	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig98575	AUGUSTUS	CDS	3009	3199	0.87	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig98575	AUGUSTUS	CDS	4604	4739	0.91	+	2	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ggcacagatggaaatcagaagattacaaagttcctgtccctggataaatgtttacccagaagaaagttcttacagattt
# tagacataccacatgatgcagataagccaatgaaaattgagctggatcctgaatggcttgtcattttgaagtctaccaatcatctactgaaccttacc
# aagatggttagatacatgcctggtcctggttccagtgaaaggtgggatttcacagtgacaaatgaagagatcaaccagatactggaggactttggtgg
# agatttgtcactgccagaaaattttaagaaaactgcagccattcataatccaaacgaagcaatgaagaatgccccaccatctcttactaccaacccac
# aaacaactctactttgtaccatgttggatcttacagatccaaatgcagtattcttgggtaaagactcacgcatcaagatagaggatttgtctgcagtg
# gaatcagctgaagacgtggaaagtgagacagctgagggtgatgatgaaggagatggggtggatgatgatgatga]
# protein sequence = [GTDGNQKITKFLSLDKCLPRRKFLQILDIPHDADKPMKIELDPEWLVILKSTNHLLNLTKMVRYMPGPGSSERWDFTV
# TNEEINQILEDFGGDLSLPENFKKTAAIHNPNEAMKNAPPSLTTNPQTTLLCTMLDLTDPNAVFLGKDSRIKIEDLSAVESAEDVESETAEGDDEGDG
# VDDDD]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370N7W.prfl --predictionStart=0  --predictionEnd=20444  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig9857520180911_busco_2432604931_.temp