# 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..424]--> unknown_A (33) <--[0..24]--> unknown_B (14) <--[0..1]--> unknown_C (18) <--[2..55]--> unknown_D (19) <--[1..23]--> unknown_E (10) <--[2..17]--> unknown_F (8) <--[4..43]--> unknown_G (32) <--[2..18]--> unknown_H (13) <--[0..75]--> unknown_I (15) <--[2..13]--> unknown_J (16) <--[10..54]--> unknown_K (10) <--[0..47]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5393420180911_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 = 14716, name = Contig53934) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig53934	AUGUSTUS	gene	1	4605	0.24	+	.	g1
Contig53934	AUGUSTUS	transcript	1	4605	0.24	+	.	g1.t1
Contig53934	AUGUSTUS	intron	1	378	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig53934	AUGUSTUS	intron	514	1704	0.55	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig53934	AUGUSTUS	intron	1802	4500	0.36	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig53934	AUGUSTUS	CDS	379	513	0.9	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig53934	AUGUSTUS	CDS	1705	1801	0.54	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig53934	AUGUSTUS	CDS	4501	4605	0.69	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig53934	AUGUSTUS	stop_codon	4603	4605	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [acctcgtaacaaagtggtggccgactttggatgcggcgatgcaaaacttgccagaagtgttcgacagaaagtgcactca
# tttgacttggttgcactgaacgattttgtgactgcttgtgacatgtctcatgtaagtggacaacttaaaattgctgaggttgccagtagattccaaag
# tcttccacaattcctgctgcaaattgaacagtttggcttccaccaactgtcaaaggacacaacaaacaaaatgttctacattttcaatttcaagaaaa
# caggaaaacctaaagtcaaaccttgcactgactctccagccttggctgtaccaaaaagatga]
# protein sequence = [PRNKVVADFGCGDAKLARSVRQKVHSFDLVALNDFVTACDMSHVSGQLKIAEVASRFQSLPQFLLQIEQFGFHQLSKD
# TTNKMFYIFNFKKTGKPKVKPCTDSPALAVPKR]
# end gene g1
###
# start gene g2
Contig53934	AUGUSTUS	gene	5250	9906	0.37	-	.	g2
Contig53934	AUGUSTUS	transcript	5250	9906	0.37	-	.	g2.t1
Contig53934	AUGUSTUS	stop_codon	5250	5252	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	intron	5421	6918	0.67	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	intron	6992	7320	0.84	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	intron	7384	8190	0.84	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	intron	8342	8686	0.99	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	intron	8805	8957	0.94	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	intron	9081	9225	0.93	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	CDS	5250	5420	1	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	CDS	6919	6991	0.91	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	CDS	7321	7383	0.84	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	CDS	8191	8341	0.99	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	CDS	8687	8804	1	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	CDS	8958	9080	0.93	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	CDS	9226	9906	0.72	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig53934	AUGUSTUS	start_codon	9904	9906	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgtttgatgaccacgctaagaagtaccgctggtttctactacccagtgaagcagcagacatcttggccggacacatcg
# ttccgaacttctcctcacaactgctcttttgtcctccctctctccgggaggttttagggttacctccctttgtcatggaggtgatgaagaatgatggg
# gtagtgcacatccctacaatagtagaccaatcagaaagcaccacccataatggcttctcagaaaaactactgcaagatttagagagagggtatggtga
# acaaagtgatcctgaaaattctggagctcaggctaattactgtgataaagacctaaaaccatgcataggagagacacaggggtgtgaatttacagaga
# gaaaaagaaaggatatctgtgatagccattctgtgcccacatcaaatacagtgtgtcctcttatcaatccatcaaggaaacgagatttacagaagaaa
# agtgtggacagttcatctttgtgtaccggtagtacttgttcagattcaaaacagaaaaaaattgacaagacacaagggataaagcaaaataatgctga
# tgaaggaaaagattccactagtgctaccagttctgaacctttgtccaagaagaaatcagcagcaagtaaatggttctctcctcccaaatccatcttta
# caaaattcctcaagggtgtggaggactacagcatgcttcgtgatggggatcgtgtgttggtctgtctgtccggtggtaaggactctttgtcactgcta
# cataccatcagacaataccagttctactgtaaagcaaaggggctgcggtttgaatttggagcagtaactgtggatccccagactccctcctatgaccc
# cagtcctctcaaacagtacttggccagtctaaatgtaccatactattacgagtctcaatgcatcatggatcaagcgcagagtctggagaattgtgcat
# ctatctgtagtttctgcagccgaatgaagcggggcaggatttatgcctgtgccaggaaaaataactacaatgttcttgctttgggacaacatttagat
# gatttatgtgaaagttttctcatgtctttcttccacaatgggatcttgaggacaatgaaggctcattatgatgtagaagaaggagacttgagggtaat
# aaggccttttgtgtatgtcagagaaaaagatctacgactttttgcagaaaaggaaagacacagaacgaagcagttactggcagctcaggaaatcttgt
# ttccgaatttgtacaacagcatgatggcggccatgaaaccgatcatggccattaacaaaactggagtacgggtcagtgacttcctgacccctaaaggg
# gaggagactgatgatatggacttttaa]
# protein sequence = [MFDDHAKKYRWFLLPSEAADILAGHIVPNFSSQLLFCPPSLREVLGLPPFVMEVMKNDGVVHIPTIVDQSESTTHNGF
# SEKLLQDLERGYGEQSDPENSGAQANYCDKDLKPCIGETQGCEFTERKRKDICDSHSVPTSNTVCPLINPSRKRDLQKKSVDSSSLCTGSTCSDSKQK
# KIDKTQGIKQNNADEGKDSTSATSSEPLSKKKSAASKWFSPPKSIFTKFLKGVEDYSMLRDGDRVLVCLSGGKDSLSLLHTIRQYQFYCKAKGLRFEF
# GAVTVDPQTPSYDPSPLKQYLASLNVPYYYESQCIMDQAQSLENCASICSFCSRMKRGRIYACARKNNYNVLALGQHLDDLCESFLMSFFHNGILRTM
# KAHYDVEEGDLRVIRPFVYVREKDLRLFAEKERHRTKQLLAAQEILFPNLYNSMMAAMKPIMAINKTGVRVSDFLTPKGEETDDMDF]
# end gene g2
###
# start gene g3
Contig53934	AUGUSTUS	gene	11528	14640	0.1	-	.	g3
Contig53934	AUGUSTUS	transcript	11528	14640	0.1	-	.	g3.t1
Contig53934	AUGUSTUS	stop_codon	11528	11530	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig53934	AUGUSTUS	intron	11564	13422	0.1	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig53934	AUGUSTUS	intron	13588	14622	0.96	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig53934	AUGUSTUS	CDS	11528	11563	0.1	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig53934	AUGUSTUS	CDS	13423	13587	0.61	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig53934	AUGUSTUS	CDS	14623	14640	0.98	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig53934	AUGUSTUS	start_codon	14638	14640	.	-	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atggagtacagaccccaggtgagaagagaaaactacagatttttacaggagcctgaatttcgtgaggaaggaggaacac
# cagctattgttgaatccatcagagcaggcctagtgttccagctcaaaaatgcagtgtcagcacaaaaaatcatggagaaggaggaacattttcacagg
# tgcaaagcagaagacacagaggctggacaggacaaacactaa]
# protein sequence = [MEYRPQVRRENYRFLQEPEFREEGGTPAIVESIRAGLVFQLKNAVSAQKIMEKEEHFHRCKAEDTEAGQDKH]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370RCS.prfl --predictionStart=0  --predictionEnd=20784  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5393420180911_busco_2432604931_.temp