# 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
# --[8..201]--> unknown_A (16) <--[0..7]--> unknown_B (33) <--[0..3]--> unknown_C (45) <--[0..1]--> unknown_D (15) <--[7..8]--> unknown_F (12) <--[0..1]--> unknown_G (22) <--[3..13]--> unknown_H (38) <--[3..25]--> unknown_I (24) <--[1..5]--> unknown_J (16) <--[9..25]--> unknown_L (29) <--[0..71]--> unknown_M (20) <--[0..1]--> unknown_N (13) <--[12..47]--> unknown_P (23) <--[5..7]--> unknown_Q (21) <--[12..70]--> unknown_T (22) <--[0..160]--> unknown_U (34) <--[0..2]--> unknown_V (8) <--[0..6]--> unknown_W (25) <--[1..3]--> unknown_X (29) <--[0..37]--> unknown_Y (15) <--[9..49]--> unknown_AA (23) <--[3..25]--> unknown_AB (10) <--[4..6]--> unknown_AC (12) <--[37..595]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig450420180911_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 = 10812, name = Contig4504) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig4504	AUGUSTUS	gene	1307	10812	0.1	-	.	g1
Contig4504	AUGUSTUS	transcript	1307	10812	0.1	-	.	g1.t1
Contig4504	AUGUSTUS	stop_codon	1307	1309	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	intron	1547	2263	0.36	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	intron	2271	3110	0.49	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	intron	3260	3530	0.83	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	intron	3610	8564	0.32	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	intron	8808	10328	0.77	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	intron	10421	10812	0.73	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	CDS	1307	1546	0.31	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	CDS	2264	2270	0.49	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	CDS	3111	3259	0.89	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	CDS	3531	3609	0.52	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	CDS	8565	8807	0.98	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig4504	AUGUSTUS	CDS	10329	10420	0.76	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gagcctgtcaagcaagctggttctccgtttacaggcgttatctccaggtgctttgaacaacacctcgatatttacattg
# attcacaagataagaatttagcggaattgataaaccgatttttggaggatttaaggcagcatggtacccctagaatggagacagaggagagcagcaat
# gtactgcccagctgtgcagatttatttgtgttctacaaaaagtgcatggttcaatgctcgcagctaagtacaggccagcccatgattgatctcaccag
# gacattccaaaaatacctcagagaatacgccaaccgagttcttctgaacaatctgcccaatgtaatatccaactgtatacagttgttggtacaagatc
# tggagacagcctgcgaaccagcacttacagcaatgagcaagatgtcgtggtcctccgttgagtcggtgggagatcaaagtggttacatatcggccatc
# actggccatttaaaacaaaacctaccagtcataagggacaatctggcatcgtctcgaaaattcttcacacagttttgtctgaagtttgtcaaaaataa
# gttttcaacgatgctcccgttgtcccacataaacatgatctggcgtgactggaaacatgccatcatgcagtcactcatggctgtaatggcccagtgcg
# gtggtgaaaatttgatttacactttagagacttacaaatatcgtactaaatccagacgaaggcacctttttcagctagagagcaagcagtgtaccaca
# tttgcacagctgaagaagagtgcgtcttgtacagagttgatttaa]
# protein sequence = [EPVKQAGSPFTGVISRCFEQHLDIYIDSQDKNLAELINRFLEDLRQHGTPRMETEESSNVLPSCADLFVFYKKCMVQC
# SQLSTGQPMIDLTRTFQKYLREYANRVLLNNLPNVISNCIQLLVQDLETACEPALTAMSKMSWSSVESVGDQSGYISAITGHLKQNLPVIRDNLASSR
# KFFTQFCLKFVKNKFSTMLPLSHINMIWRDWKHAIMQSLMAVMAQCGGENLIYTLETYKYRTKSRRRHLFQLESKQCTTFAQLKKSASCTELI]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937092W.prfl --predictionStart=0  --predictionEnd=28809  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig450420180911_busco_2432604931_.temp