# 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
# --[33..161]--> unknown_A (24) <--[0..2]--> unknown_B (12) <--[0..4]--> unknown_C (65) <--[1..5]--> unknown_D (51) <--[0..17]--> unknown_E (15) <--[0..2]--> unknown_F (67) <--[0..12]--> unknown_G (15) <--[0..21]--> unknown_H (18) <--[0..2]--> unknown_I (10) <--[7..12]--> unknown_K (17) <--[0..6]--> unknown_L (12) <--[0..1]--> unknown_M (15) <--[11..18]--> unknown_O (51) <--[2..8]--> unknown_P (56) <--[0..3]--> unknown_Q (31) <--[0..6]--> unknown_R (23) <--[0..3]--> unknown_S (25) <--[0..6]--> unknown_T (74) <--[0..1]--> unknown_U (82) <--[0..2]--> unknown_V (98) <--[50..460]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2874920180911_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 = 18353, name = Contig28749) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig28749	AUGUSTUS	gene	9379	15924	0.03	+	.	g1
Contig28749	AUGUSTUS	transcript	9379	15924	0.03	+	.	g1.t1
Contig28749	AUGUSTUS	start_codon	9379	9381	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig28749	AUGUSTUS	intron	13219	14526	0.06	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig28749	AUGUSTUS	intron	14682	15053	0.38	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig28749	AUGUSTUS	intron	15185	15679	0.82	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig28749	AUGUSTUS	CDS	9379	13218	0.08	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig28749	AUGUSTUS	CDS	14527	14681	0.09	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig28749	AUGUSTUS	CDS	15054	15184	0.4	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig28749	AUGUSTUS	CDS	15680	15924	0.93	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig28749	AUGUSTUS	stop_codon	15922	15924	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcatgcgatattccaagagaaattttagttcaaaaatcgtcaagttctccacaagaatgcttgaaatacatcacct
# ctgttctctcgaccctggaaaagtacatccagagaagtgtacctggacccccagtgtgctcagaagaggatgtttgtctaatgaaaatcattttcaaa
# gcattgaactgtccatcaaaccgcgaactaactgtagaggtactgaacctattcagagaaacccgggccgttgactatttgataggactgctgagcgc
# gttagaggtggatacctgtacggaagacagcgcggatatcctcactacggtagtggaaatactggatcagttacaatcatgcatgcccagttcctcat
# tacagttacagggcttgatctgtgtgctggaagacactataaagaagaccaaagcatccagaaaactccaacaaagaatttccgcgataaaagagagc
# atacacaggtcgataaatgcacagaaacgaaaagttgttgcaaaggaaaatgtggatagacgcaaaccgcctggggacttcaggaaaatacccatata
# tccgagaagagatgatatatttcccgaccagaaacctttcctgcgaaaagtgatcagggatggacgttatgatgatttagagcattatttggacgtcc
# agtttcgactcttcagagaggactgtatagcacaactcagaatgggtgtacaggagtatagacaagaacacgaagacggaaattacgttagacagcta
# gagaatgcccggatttataatgatgttaggattttattcagggaaacatctttggatggaatcctgcatgttgtacagcttccagagagaacttatca
# aaacattgactggaacaatacaaagagactgatccatggcactcttgtctgcttgtcattggatcatttcaaaacttttgcatttgcaaccatttttg
# cggcagaatcgaacattttagaaattagaggaatattcaagattaagatggtctcagaaagtaatgcaataaaagggaacatgttgggatgcctgtgt
# aaaatgatagaaagcacagcactttttgaagcctacagatatggactagaaaagttacaaaacacaagaccgggacaattagcttttgagaaatatat
# tgtgagatgcgagacaaacattggaaaagcggagtatatggaagaggataaaatgtacgacctttcatcaattatcaagaactgtccagtaaaacgca
# acaatgtcaaccgatatcaaggaatccgacgattgtcggatacaaccagttggccctctggtgacgaacttcgaatgaacccctctcagtatgaggcc
# tttaagtcggcgttgacaaaggaattctgtattatccagggacccccaggcacagggaaatcttatctgggacttcaaattgtcaaaacattgctagc
# aaacacttcctgctggtctgctggtagaaattatccaatcattctggtttgtttcactaatcacgcattggaccagtttttagaaaatatattatgtt
# ctgttgatgaagggtataaggataaaattgttcgagttggtggtcggagtaaaaccgaaaccattgaagccatttcacttaggaaaaagagtgagaga
# acatacaaaaagaggaggttactttctttacatttacttcagtcgttgatttccagaaatacagaaatgatagatagattacctttcaccattgttga
# tcacatcactttggcgatgtacgttgcactgccgagagagcaattcttgcgacaagatgaaacatcgatgttcagatggttaaatgtcgatgacgagg
# gaattctgaactccgcaggaagcaaagagtggaatggaaaccatccaaatcttttagaatatgtcgagcaagaaaacaatatgcacaaaaatgaatat
# gaaaatgcatatcacggtcttacatcaagcgtagaactgagtgaatttcctgatttgagaattaaagaattcccatatggtcagtttgggatgaatat
# tcttgcgatgtggcgtagattatcgagagaaccaaacacagaacttcgaaagaaaattaaatgcgaaattggcaacattcttggagaaatgaattcgg
# gtgatgtcatatctgataatgtggctgcactgtacgaaaagcagaatctgtggaatctatccatcccaaacagatggaaattatacagatactggaaa
# aacaaattttgcagaagtataatgacgaaaacggaggcctttaaagcacatcagggtgacataatagaatattacaaagacgaaaaatttatgaaaga
# attcagtgttcttaatagagctgctcttattgcaatgaccacaacaggagctgcaaaataccacaggatgctacaacttcttcaaccacgcattacaa
# taattgatgaagcagcagaagtgttagaggcccacattttggcttcactcacgtcctcgtgtcaacatttgatactgataggtgatcacaaacaactg
# gagccgaagcctgcagtttacgaacttgctcagaagtaccacatgtcactatcattctttgaaaggatgattcgtaatggtgtaccctatcactgctt
# gttgaaacaacatagaatgagacccgatatttctatagtagtaaaggaaatttatccaggtcttcatgatgctgaaaacgtggaaaaatatgaacatg
# ttggtggagttggaaaagatgttttctttttgaatcacgaattcaaagaaagctatcaagaggagggaagaagttatgaaaatgcatatgaagctgca
# ttcactgcacgtttgtgcgagtatttacttttccagggctataagtcttctcaaattacaatactgacaccatattcaggtcaggtgcgatgtttgtc
# aaactttgtgaacactaagataaaagacgtacggatcagcatagtggacaactaccaaggggaggaaaatgacatcgttttattgtccatggttagaa
# gtaatgatattgggaagctagggtttttggataaggagaatagagtttgtgttgctttgtcgagggcaaggataggtctgtttgtcattggaaatttt
# gacatgatgtgcacgaatgcgaagaaaacgcaatattggaagactgtagttaaaattctaaaagagaaaggatgttttggaacagaactccctctctt
# ctgtcagaatcaccctaaacgtcaaattcaagcgataaatgcacatgatttcgataattgtccagagggagggtgtcaagtcaaatgtgatgccagac
# tacagtgcggtcactcgtgcagaagatattgtcatccagaagacaaggagcacacgtcatacatttgctatgtacagtgcctttctacgtgcacctct
# gggcacacgtgtaaccaactttgtcattttccagatccatgtaattgtaaagcattggtggataaagcgtttcaatgtgggcatgtcaacacaataga
# atgctattgtgaccctaacaaagaaaaatgtgataaaatcgtcacaaagtatttcagaaactgtggacatagtatagaaattccgtgttatgcccctg
# taaacgaatatacgtgtgaagaaatagttgaacgtgaactcttgtgtggacacacagctacagttcagtgtcacgtcgaagtttcaagcacagattgc
# acggagcttatggaaaagaaatggtcatgcggtcattcagcccaaatacaatgcagatatttcagttcagcaaactgtacagaagaggttgttcgaat
# gctcgagtgtggtcatgagaattggatgaaatgccatctagaagggaattcatgcttggtgtatctccctgactgtaaacattgtttcgaagctagtg
# tactggatgatttcatagcgcagatgaaaccacaagaatccctgaaatgcctctcttgtccaaaatgccgtacacggatcacgtggcatccaagccag
# taccaggaacccagttacgtcgtgaatgtgtgtcataattcaccattgatggatagagcagttacgttaccaaatattgcattaatggcagatccaca
# tatggaaaactggaaagtgtgcaaggaagaaaggggcttgggcatggacagtttggattcactatcacaagatgataagtcagcgattgatatggaaa
# acacaggtgcacggccaaaggactttaaaagaaatgcaccagggggccaggatgatggaaagactgaagctaaaacagaaacagctaaacctagaaag
# ggggaaaagtctagggaaaaagcgatgccaaaatggaaaaagaaaccgtcgaaaaaatggtgggaggaaaaattgtga]
# protein sequence = [MACDIPREILVQKSSSSPQECLKYITSVLSTLEKYIQRSVPGPPVCSEEDVCLMKIIFKALNCPSNRELTVEVLNLFR
# ETRAVDYLIGLLSALEVDTCTEDSADILTTVVEILDQLQSCMPSSSLQLQGLICVLEDTIKKTKASRKLQQRISAIKESIHRSINAQKRKVVAKENVD
# RRKPPGDFRKIPIYPRRDDIFPDQKPFLRKVIRDGRYDDLEHYLDVQFRLFREDCIAQLRMGVQEYRQEHEDGNYVRQLENARIYNDVRILFRETSLD
# GILHVVQLPERTYQNIDWNNTKRLIHGTLVCLSLDHFKTFAFATIFAAESNILEIRGIFKIKMVSESNAIKGNMLGCLCKMIESTALFEAYRYGLEKL
# QNTRPGQLAFEKYIVRCETNIGKAEYMEEDKMYDLSSIIKNCPVKRNNVNRYQGIRRLSDTTSWPSGDELRMNPSQYEAFKSALTKEFCIIQGPPGTG
# KSYLGLQIVKTLLANTSCWSAGRNYPIILVCFTNHALDQFLENILCSVDEGYKDKIVRVGGRSKTETIEAISLRKKSERTYKKRRLLSLHLLQSLISR
# NTEMIDRLPFTIVDHITLAMYVALPREQFLRQDETSMFRWLNVDDEGILNSAGSKEWNGNHPNLLEYVEQENNMHKNEYENAYHGLTSSVELSEFPDL
# RIKEFPYGQFGMNILAMWRRLSREPNTELRKKIKCEIGNILGEMNSGDVISDNVAALYEKQNLWNLSIPNRWKLYRYWKNKFCRSIMTKTEAFKAHQG
# DIIEYYKDEKFMKEFSVLNRAALIAMTTTGAAKYHRMLQLLQPRITIIDEAAEVLEAHILASLTSSCQHLILIGDHKQLEPKPAVYELAQKYHMSLSF
# FERMIRNGVPYHCLLKQHRMRPDISIVVKEIYPGLHDAENVEKYEHVGGVGKDVFFLNHEFKESYQEEGRSYENAYEAAFTARLCEYLLFQGYKSSQI
# TILTPYSGQVRCLSNFVNTKIKDVRISIVDNYQGEENDIVLLSMVRSNDIGKLGFLDKENRVCVALSRARIGLFVIGNFDMMCTNAKKTQYWKTVVKI
# LKEKGCFGTELPLFCQNHPKRQIQAINAHDFDNCPEGGCQVKCDARLQCGHSCRRYCHPEDKEHTSYICYVQCLSTCTSGHTCNQLCHFPDPCNCKAL
# VDKAFQCGHVNTIECYCDPNKEKCDKIVTKYFRNCGHSIEIPCYAPVNEYTCEEIVERELLCGHTATVQCHVEVSSTDCTELMEKKWSCGHSAQIQCR
# YFSSANCTEEVVRMLECGHENWMKCHLEGNSCLVYLPDCKHCFEASVLDDFIAQMKPQESLKCLSCPKCRTRITWHPSQYQEPSYVVNVCHNSPLMDR
# AVTLPNIALMADPHMENWKVCKEERGLGMDSLDSLSQDDKSAIDMENTGARPKDFKRNAPGGQDDGKTEAKTETAKPRKGEKSREKAMPKWKKKPSKK
# WWEEKL]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093701S0.prfl --predictionStart=0  --predictionEnd=32591  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2874920180911_busco_2432604931_.temp