# 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..40]--> unknown_A (37) <--[0..8]--> unknown_B (18) <--[4..14]--> unknown_C (23) <--[25..302]--> unknown_G (34) <--[3..93]--> unknown_H (22) <--[8..12]--> unknown_J (37) <--[5..13]--> unknown_K (14) <--[0..2]--> unknown_L (41) <--[0..1]--> unknown_M (19) <--[2..4]--> unknown_N (12) <--[0..2]--> unknown_O (22) <--[0..1]--> unknown_P (42) <--[0..80]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig41020180911_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 = 20660, name = Contig410) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig410	AUGUSTUS	gene	7882	14753	0.01	+	.	g1
Contig410	AUGUSTUS	transcript	7882	14753	0.01	+	.	g1.t1
Contig410	AUGUSTUS	start_codon	7882	7884	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig410	AUGUSTUS	intron	8295	9616	0.6	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig410	AUGUSTUS	intron	9759	10046	0.52	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig410	AUGUSTUS	intron	10174	11914	0.05	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig410	AUGUSTUS	intron	11997	14017	0.21	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig410	AUGUSTUS	CDS	7882	8294	0.43	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig410	AUGUSTUS	CDS	9617	9758	0.48	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig410	AUGUSTUS	CDS	10047	10173	0.15	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig410	AUGUSTUS	CDS	11915	11996	0.84	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig410	AUGUSTUS	CDS	14018	14753	0.16	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig410	AUGUSTUS	stop_codon	14751	14753	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaggcgaacaagttcatatgctgttgctgataaaaagactgacaatgaaagtgaactgccatcatctgacgctactc
# tgaaaaggtaccgatgtcttcgtgtgtcgggaaaacaaagggcagacaactccatggaggatgaggcggatgaacatgagagtgaagatgcaccagcc
# gaactggtgtccgatctctcacagaggaagaacacgaatgtagagagagaaagcgcacagaggcgagcgctatactcccgccgcttctccgagccggg
# aaaagtcctcatgtccaccggtcaaaccgatccgcgattccggcgcagccagagccaagtggaccagacaatgttaaacaaacaaatattgcacaaca
# gggttataatgttaagacaaacagatagcatgacagagtgtgtgctgcctgttgcaggtcagaaagacatctctgttgtttatgacaggttttattgt
# gcagtgtgtcgtgctgtgcagtcagaagacgatctgtttgtttatgacagttttttaaattgtgcagctgtgtggcttgtgtcatgtgcttgcctgtg
# cagtcaggaagacgatctgtttgtttatgagctgtttttaacttgtgcagtgtgttgcctgtgcagtccagaagacatctgttttgtttatgaccgtt
# ttaactgtggcgagtgtgcccaggtggcgaccagtttactgcagcagagagccaatgatgtcagagctaacagggtcaactggcagagctatgttcaa
# tacaatcaccacagaaatcagttacattcacccacagaaatcagtacatcaccacagaaatcagacatcaccacagaaatcagtacatcaccacagaa
# gaaaatcagctacatcaccatcagaatcagtacatcaccacagaaatcagtacaacagaaatcagttatcaacaccacagcaaagcagacatcaccac
# agaaatcagtacaacaccacagaaaatcagttagcatcaccacagaaatcagtaatcaccacagaaatcagtacatcaccaatataaatcagtacaca
# ccacagaaatcagttacacagaaatcagtacatcaccacagaaatcagtacatcaccacagaaatcagtactacacaaatcagtacatcaccacacag
# aaatcagtacatcaccacagaaatcagttacatcaccacagaaatcagtacatcaccaccagacaatcagtacatcacgcacagaaatcgtacatcac
# cacagaaatcagttacatcaccacagaaatcagtacatcacacacagaaatcagttacatcaccacgtgaaattcagtacatcaccacagaaatcagt
# acatcaccacaagaaatcagtacatcacagaaatcagtacatcacacagaaatcagatccacaacagaagaatcagtacatcaccacagaaatcagta
# caacagaaatctgagtaacaattcactcacgagaaagagttcaagttga]
# protein sequence = [MRRTSSYAVADKKTDNESELPSSDATLKRYRCLRVSGKQRADNSMEDEADEHESEDAPAELVSDLSQRKNTNVERESA
# QRRALYSRRFSEPGKVLMSTGQTDPRFRRSQSQVDQTMLNKQILHNRVIMLRQTDSMTECVLPVAGQKDISVVYDRFYCAVCRAVQSEDDLFVYDSFL
# NCAAVWLVSCACLCSQEDDLFVYELFLTCAVCCLCSPEDICFVYDRFNCGECAQVATSLLQQRANDVRANRVNWQSYVQYNHHRNQLHSPTEISTSPQ
# KSDITTEISTSPQKKISYITIRISTSPQKSVQQKSVINTTAKQTSPQKSVQHHRKSVSITTEISNHHRNQYITNINQYTPQKSVTQKSVHHHRNQYIT
# TEISTTQISTSPHRNQYITTEISYITTEISTSPPDNQYITHRNRTSPQKSVTSPQKSVHHTQKSVTSPREIQYITTEISTSPQEISTSQKSVHHTEIR
# STTEESVHHHRNQYNRNLSNNSLTRKSSS]
# end gene g1
###
# start gene g2
Contig410	AUGUSTUS	gene	14885	25180	0.01	+	.	g2
Contig410	AUGUSTUS	transcript	14885	25180	0.01	+	.	g2.t1
Contig410	AUGUSTUS	start_codon	14885	14887	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	intron	14978	15496	0.86	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	intron	15587	15909	0.99	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	intron	16024	18789	0.87	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	intron	18895	19620	0.4	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	intron	19634	21383	0.24	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	intron	21443	21595	0.3	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	intron	21622	22107	0.62	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	intron	22219	22464	0.65	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	intron	22554	23624	0.51	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	intron	23794	24547	0.62	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	intron	24674	25074	0.45	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	14885	14977	0.3	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	15497	15586	0.86	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	15910	16023	1	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	18790	18894	1	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	19621	19633	0.4	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	21384	21442	0.32	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	21596	21621	0.6	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	22108	22218	0.97	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	22465	22553	0.37	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	23625	23793	0.76	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	24548	24673	0.5	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	CDS	25075	25180	0.99	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig410	AUGUSTUS	stop_codon	25178	25180	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgatttcccaggaagactacaattttatttaccaatttgacaatgctaacaacgagactaaaactgccatgttgaggg
# aagctgggccacagtttgccaggactttctttaatctaatgagtcagatcgctaaggaccagactctacagtacattctcactatgatggatgatgta
# ttacaggaggacaaagcccgagtggagatactgaaggagtatgccaaacagatgaaggaatcagtatggacaccatttatgcatctcctgaacagaaa
# tgacagatttatcgtgaatcagaccagtagaatcattgctaagattgcctgttggagtaaagaattgatggggctggatgacttgaagttttacatgg
# actggctcaaaaatcaactaaggcttccaaacaccgaaatagatataacgggacgggatgctttgcaagtgtgtagattatcaacgggatggaatccc
# tacatagaaacgaggaacggaatcactacgatcgtgtcggtgctgctgggaagtaaggttggctttcagatccagtatcagctgattttctgtctgtg
# gtgtctcagcttcagctcgcacatagcagagagaatgagcaaagataaaataatccccgtgttatcagacattctcagtgagtcggtgaaggaaaaag
# tctccagaattatcctggccacgtttagggtagaaaagcccgaggaaagggatttggtccatgaacacgccgtggcgatggtgcaatgtaaggttctg
# aaacagctagaattactggaatccaggaagtttgatgatccggatattgtggatgacctggagttccttaacgagaaactacaggagtctgtccaaga
# cctcagctctttcgatgaatacacatccgagatcaaatccgggaggctggagtggagccccgttcacaagaatgaaaagttttggcgggagaatgcaa
# tcagacttaatgaaaataattactctctccttaagatgttagttagactcttagaaagtagcaaagatcccttaattttgtccgtcgctgctcacgac
# ctcggggagtatgtcaggcattatccacgaggaaaagtgtaa]
# protein sequence = [MISQEDYNFIYQFDNANNETKTAMLREAGPQFARTFFNLMSQIAKDQTLQYILTMMDDVLQEDKARVEILKEYAKQMK
# ESVWTPFMHLLNRNDRFIVNQTSRIIAKIACWSKELMGLDDLKFYMDWLKNQLRLPNTEIDITGRDALQVCRLSTGWNPYIETRNGITTIVSVLLGSK
# VGFQIQYQLIFCLWCLSFSSHIAERMSKDKIIPVLSDILSESVKEKVSRIILATFRVEKPEERDLVHEHAVAMVQCKVLKQLELLESRKFDDPDIVDD
# LEFLNEKLQESVQDLSSFDEYTSEIKSGRLEWSPVHKNEKFWRENAIRLNENNYSLLKMLVRLLESSKDPLILSVAAHDLGEYVRHYPRGKV]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370E8S.prfl --predictionStart=4540  --predictionEnd=45174  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig41020180911_busco_2432604931_.temp