# 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
# --[10..473]--> unknown_A (19) <--[31..133]--> unknown_C (33) <--[5..6]--> unknown_D (9) <--[0..1]--> unknown_E (11) <--[7..23]--> unknown_F (14) <--[51..303]--> unknown_J (19) <--[0..6]--> unknown_K (16) <--[16..72]--> unknown_M (18) <--[9..26]--> unknown_O (19) <--[9..154]--> unknown_P (25) <--[0..25]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig12195420180911_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 = 5820, name = Contig121954) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig121954	AUGUSTUS	gene	1	1269	0.85	+	.	g1
Contig121954	AUGUSTUS	transcript	1	1269	0.85	+	.	g1.t1
Contig121954	AUGUSTUS	intron	1	940	0.85	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig121954	AUGUSTUS	CDS	941	1269	0.85	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig121954	AUGUSTUS	stop_codon	1267	1269	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [agactccatcggatatagagccagctgatacagatctcacgatcaattgtgacaaaccaacaaaatcagagatcaggag
# agctattaccacacttaagaatggaaaatcaccagggcctgatgaaataccagcagaagccatcaaagctgacactgagacagctatagacatcctgt
# ataacctcttcaagaagatctggaaggaagagaacatccgtgaaaattggaaagagggtaatatcctcattatgctgccaaagaagggagatttgagg
# gactacaataactatcgaggaataatgttcctgtcagtgcctggcaaaccttaa]
# protein sequence = [TPSDIEPADTDLTINCDKPTKSEIRRAITTLKNGKSPGPDEIPAEAIKADTETAIDILYNLFKKIWKEENIRENWKEG
# NILIMLPKKGDLRDYNNYRGIMFLSVPGKP]
# end gene g1
###
# start gene g2
Contig121954	AUGUSTUS	gene	1814	3819	0.35	+	.	g2
Contig121954	AUGUSTUS	transcript	1814	3819	0.35	+	.	g2.t1
Contig121954	AUGUSTUS	start_codon	1814	1816	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig121954	AUGUSTUS	intron	2217	3721	0.35	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig121954	AUGUSTUS	CDS	1814	2216	0.76	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig121954	AUGUSTUS	CDS	3722	3819	0.58	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig121954	AUGUSTUS	stop_codon	3817	3819	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggagcagagacatggagaactactaaaacagccccgcaaagatccagacattttcacaacacctgtctcaggcgcat
# ccttaacatccgatggcctgaaaggatcacaaatgaagaactatgggaggagagcaaatcaagaaaccaatggacatgcaaatcaggcagaggaagtg
# gggttagattggacacactttgaggaagccaccaaccaacaccacacgacaggccctgacttggaaccctcaggcagagaaagagaggatgtcctaga
# aacactggtcgcgagacatggagtcagaattgagagaacatggcaccacctggaagagcagcccagaacggtgttcgctggaggactttcgttgatgg
# cctatgttccccacggaacgttaggcctaaggcgagcgagtaggagcgactatgaaaaaggcagaaactacgatgtattgtaccctgatcaatacgta
# gccagctcagaggtcggccggcaatgttga]
# protein sequence = [MEQRHGELLKQPRKDPDIFTTPVSGASLTSDGLKGSQMKNYGRRANQETNGHANQAEEVGLDWTHFEEATNQHHTTGP
# DLEPSGREREDVLETLVARHGVRIERTWHHLEEQPRTVFAGGLSLMAYVPHGTLGLRRASRSDYEKGRNYDVLYPDQYVASSEVGRQC]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370GHP.prfl --predictionStart=0  --predictionEnd=23172  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig12195420180911_busco_2432604931_.temp