# 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
# --[12..203]--> unknown_C (13) <--[12..34]--> unknown_E (11) <--[5..8]--> unknown_F (20) <--[0..3]--> unknown_G (9) <--[0..3]--> unknown_H (27) <--[10..23]--> unknown_J (33) <--[0..3]--> unknown_K (52) <--[0..1]--> unknown_L (46) <--[3..11]--> unknown_M (27) <--[0..2]--> unknown_N (13) <--[0..1]--> unknown_O (10) <--[0..3]--> unknown_P (21) <--[1..19]--> unknown_Q (47) <--[1..16]--> unknown_R (20) <--[8..27]--> unknown_T (33) <--[0..90]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4550620180911_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 = 16055, name = Contig45506) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig45506	AUGUSTUS	gene	1543	3183	0.2	+	.	g1
Contig45506	AUGUSTUS	transcript	1543	3183	0.2	+	.	g1.t1
Contig45506	AUGUSTUS	start_codon	1543	1545	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig45506	AUGUSTUS	intron	1568	1796	0.65	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig45506	AUGUSTUS	intron	2004	2605	0.99	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig45506	AUGUSTUS	intron	2786	3124	0.31	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig45506	AUGUSTUS	CDS	1543	1567	0.62	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig45506	AUGUSTUS	CDS	1797	2003	1	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig45506	AUGUSTUS	CDS	2606	2785	0.44	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig45506	AUGUSTUS	CDS	3125	3183	0.5	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig45506	AUGUSTUS	stop_codon	3181	3183	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcaggatcaggtgccatggaggaacgtgaatgatataacgcacgtggtgaattacgactttccgctcgacttgacga
# attacgtccacagagtaggaaggacgggaagagcaggacgtaaaggcgagtccatctccttcttctcgctacacgatcagcgtaacaacgtgggaaaa
# ctggtggacatactcagggagagcaaccaggagattcccgacgaacttttagaagagacaacagaagtcgttaccatgggagcgggggcagggcttct
# acttacttcagcgacagagaaagcagtggtcgacacaacagaagccgacagcgaagtggagggagctttaggtggagggactacgaggaatgacctca
# gcggacataggggacacgcgtgggggtcgagtaagcaatatcaaatatacaatgcagatgactacaatgttcgactacataagatgcaagaactttga]
# protein sequence = [MQDQVPWRNVNDITHVVNYDFPLDLTNYVHRVGRTGRAGRKGESISFFSLHDQRNNVGKLVDILRESNQEIPDELLEE
# TTEVVTMGAGAGLLLTSATEKAVVDTTEADSEVEGALGGGTTRNDLSGHRGHAWGSSKQYQIYNADDYNVRLHKMQEL]
# end gene g1
###
# start gene g2
Contig45506	AUGUSTUS	gene	5163	16055	0.01	-	.	g2
Contig45506	AUGUSTUS	transcript	5163	16055	0.01	-	.	g2.t1
Contig45506	AUGUSTUS	stop_codon	5163	5165	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	5492	7089	0.15	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	7124	9374	0.19	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	9456	9610	0.94	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	9704	9953	0.49	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	9993	10104	0.68	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	10163	10409	0.93	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	10484	10690	0.96	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	10791	11751	0.51	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	12032	13071	0.81	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	13163	14673	0.76	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	14724	15577	0.44	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	intron	15658	16055	0.22	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	5163	5491	0.48	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	7090	7123	0.21	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	9375	9455	0.77	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	9611	9703	0.54	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	9954	9992	0.57	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	10105	10162	0.92	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	10410	10483	0.93	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	10691	10790	0.99	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	11752	12031	0.86	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	13072	13162	1	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	14674	14723	0.75	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig45506	AUGUSTUS	CDS	15578	15657	0.43	-	1	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [attcaacaaattgacagaaagatttttcaagacatctgcatggccagaggcagaagtagttgctccaattgtacagaat
# gagttgcccaatcagtgctgtgggaacatcattgatgaatttatctatcagatctggaacgtccacagtgtcctgaatgtcctacattctctcgtgga
# caagtccaacatcaacaaacagctggaggtgtactcgatgggagagcatgtattctcgggtgcctgcttgtcagatcaccacgttttattacgtgggt
# ttcgcctacctgatgatgaggaggtaccaggatgcaatcagaacgttctccaacgtcttgctgtacatccagagaacaaaacagatgttccaggctcg
# ggttcagatgtacgaccaggtaaagacttacgacttaagtttgtaaaatggtgcactgctccatcctcaacctcctcagaaaagtcagaacactgccc
# aattgctccgtttgtcattctgaggaggagagacattgaggagtttcaaaataacttctctttcgcctgccccaagttcttgtctcctgttccaccaa
# actatgatgctgtggctgccataaatcataaggaaccgttcctgctgcagctgaaggtgtttatagaggaggtgacacaacagatcgtgttacccacc
# atcagaagctacctcaagctgtacactacgctccccttgtcaaagcttgctatcttcatggacatgagtgaagatgagctgaaaacacacctgatgtg
# cttcaagcacaaaatgaagaacgtggtgtggactaaggggaccagtggtctggagggagaattccagtcagcatcagaagtggacttctacatcgaca
# aggaaatgatacacattgcggatacaaaagtggcaaggagatacggagatttcttcatcagacagattcacaagtttgaggaggacagggatacaaat
# actgctgcaataaaacctgtccctcgcactaccacgagcttatccagaggaatgcagcatccctcgcacgattacacgagagcgagccagagggatgc
# cacatccccgcacaccacgagtctgagagaaaatgcgaaatgccgcatccctcgcataccacgagctgagccaaatggaatgccagcatctctcgcaa
# tggaacaaccacgagctggccgtatcgctcgcagctaccatgaacagcttcctgcccacagacatttaccattatccaagtgtgaacataattttaac
# gctatatacacggtatggtcgaaccagctcatgtataggagtgccggatcctaa]
# protein sequence = [FNKLTERFFKTSAWPEAEVVAPIVQNELPNQCCGNIIDEFIYQIWNVHSVLNVLHSLVDKSNINKQLEVYSMGEHVFS
# GACLSDHHVLLRGFRLPDDEEVPGCNQNVLQRLAVHPENKTDVPGSGSDVRPGKDLRLKFVKWCTAPSSTSSEKSEHCPIAPFVILRRRDIEEFQNNF
# SFACPKFLSPVPPNYDAVAAINHKEPFLLQLKVFIEEVTQQIVLPTIRSYLKLYTTLPLSKLAIFMDMSEDELKTHLMCFKHKMKNVVWTKGTSGLEG
# EFQSASEVDFYIDKEMIHIADTKVARRYGDFFIRQIHKFEEDRDTNTAAIKPVPRTTTSLSRGMQHPSHDYTRASQRDATSPHTTSLRENAKCRIPRI
# PRAEPNGMPASLAMEQPRAGRIARSYHEQLPAHRHLPLSKCEHNFNAIYTVWSNQLMYRSAGS]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370ARO.prfl --predictionStart=0  --predictionEnd=33165  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4550620180911_busco_2432604931_.temp