# 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..1843]--> unknown_A (38) <--[1..5]--> unknown_B (10) <--[0..1]--> unknown_C (13) <--[0..3]--> unknown_D (45) <--[0..2]--> unknown_E (18) <--[0..2]--> unknown_F (9) <--[4..5]--> unknown_G (22) <--[3..16]--> unknown_H (9) <--[0..5]--> unknown_I (10) <--[5..44]--> unknown_J (14) <--[0..3]--> unknown_K (13) <--[0..1]--> unknown_L (26) <--[3..12]--> unknown_M (60) <--[0..1]--> unknown_N (26) <--[2..69]--> unknown_O (29) <--[22..69]--> unknown_Q (19) <--[0..531]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig1872820180911_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 = 17142, name = Contig18728) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig18728	AUGUSTUS	gene	1672	4461	0.65	-	.	g1
Contig18728	AUGUSTUS	transcript	1672	4461	0.65	-	.	g1.t1
Contig18728	AUGUSTUS	stop_codon	1672	1674	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig18728	AUGUSTUS	CDS	1672	4461	0.65	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig18728	AUGUSTUS	start_codon	4459	4461	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggagggtgaaagtattcatgcactgaagataccagagacaatccagtcaggagatgaagaatttgtcatagaaatca
# actccgactacagtgatgaagaaacggatgatgatagagaaaagagaaatgaatgggaaatgggccagtatgatgagacagattctatggaacagtgt
# actggacagaaacaccttacacataaaaatcaaagagattcccatctacagccagccaacaccgccaaagtgtccagtccactcaagataggaagaga
# ccttgatggcaaggtgaatttcattggtttggagccttccaatgatgaatctagttctgatcacatgggaaatgacatgccttcaggacttgaaaata
# ttaaaatcattaatgtttgcactcttgccgatgacttcgaacaagatactctggagaacccaagaatggagaacttcaactctgaacaatacatgaat
# gctgaaggtgaccaccaagattctgatatgccttcaagaacatcaaacatgattattattaatgagcaacattcacaaagcactctgtccatgatgct
# tgtatgcaagttttgtcatgatctttttcctactcatgaagcattacattgtcatgtcaaacagcacatggagaatgtcaaacagcataatatggaaa
# acaaagacgaacacactgaagagaaacatattttcaagcaagcaccggataaaaaattacaaaagataaatgtaaggaaggaggacacggaggaagat
# agatcacaccaagggaacaaatacgctgctaaaaaaagaaaaagccccgaaaatgacggtgttgagcgaaaatcagggagaatgaagaaaaagagaaa
# ccatggactggttgatgaggagaacaaatgtgagaagtgcggcaagattttcattaaggagtatcaatatagatcacacgtttccttctgtaaaggga
# agataactcagatggccacatgctttgaatgtaacaaaatgattccagctcatcaagagtatgaacatgctctaaaataccatgatatagtttgtcca
# atatgtggtgtaaatcaaatgaaggaatctaaactgagaaaccatatgaagttcatgcacaagatttttaattacggaaaagatacgcagaaatctga
# tataaagaatcagatttgtgtggtggaccaagtttattacaaaacatgtaatttatgtggtaaagtgtgcgcatcgtttgaagaattcaaggagcaca
# gaaaagagcacagaactttgaaacaaatggagacagctgccatcttagaaaaaacgaaagaggaagaagacaaagctcaaaaaagtcaggatcagact
# acaccggcgaagccaaagaaggagaaaccgaatcagtcctccgccatagagtgtgaaaactgcgaaaagaagttttcctctcgctaccagttagatag
# ccatctgaagagatgttctgccaaagctgtcaaagtgttgttgtgtgatgtttgtgaactgctggtgccttacgatgaacataaagagcacgtcaaat
# ctcatgaaatcatatgtgatttgtgtggaaaggtttgctatggtaaaaaaagttttaaatggcatagcatgcattgtccagcgaaacagaatatggtg
# aaagttgctaaagaagatttgatgaaaactgctgaagatttgatgaaaactgaaactcagagacctggaaaatctagtataaacaagacaaagtggaa
# aaaaaagaaaacgtggagatctattcagttgaccagaaatttgaagcgaaaatttactcaaaaacagaagatattcttggagaaagaaatgggaattg
# atactaaaacattggaagaaagtcaagttataaatagtgaattagtaagtgatatgatcaaaagaggaggcgcaccacaggatagtgaaattgaggca
# gttaaaacagcaatagttaatgaaggaatagaaaattctccaaaaagtatcaaattagagtcagaaaatcatgaggaggatagatttgatcaagacac
# tcttgaagacagagataatagtgaaagaataatgagcactggtgattttagtgatagcaagactgagagctatcctgggaaaggtggcagtcagattc
# ctgtggaaggggatgctgttgaatgtaacacgagaaaaaatgggataaatgaaaggagaaggaaaagaaggagacgaaatctttcgcgtctagggaac
# agacgaaagaaagcaaggaaacagaaaacagatcaaacgcaggagggttttgttcacttatccaatgctgtgatggagggaaagtgtgaagaagttaa
# cgcaaatataccaagggcagctggtgcaccatttgaagattcaacagaaaatgaaggcttttccagaaatacattaaggacaaaccctactaacattt
# cacgagacacatcagaaacagaatctgatattgaggaggaagaggtatatattggaattatacaaaatcgtaaaattcctacttatgagccaacaggg
# aattctgccatgttaaatttgaatgggatggaaaaaacttgtctggatgactggctgatacaaacttcaaactcacatgacaatgcccaagtctggat
# ttgtcgacattgtggaaagcagttgggttctagggaagagggctttgatcacatgattagctgccatccaaccaacaaggccacaaaagaaatcctaa
# aggaaatggagatgctaaggttgaagatgctatctaggtcacaaacagatgctgtgcttgaatga]
# protein sequence = [MEGESIHALKIPETIQSGDEEFVIEINSDYSDEETDDDREKRNEWEMGQYDETDSMEQCTGQKHLTHKNQRDSHLQPA
# NTAKVSSPLKIGRDLDGKVNFIGLEPSNDESSSDHMGNDMPSGLENIKIINVCTLADDFEQDTLENPRMENFNSEQYMNAEGDHQDSDMPSRTSNMII
# INEQHSQSTLSMMLVCKFCHDLFPTHEALHCHVKQHMENVKQHNMENKDEHTEEKHIFKQAPDKKLQKINVRKEDTEEDRSHQGNKYAAKKRKSPEND
# GVERKSGRMKKKRNHGLVDEENKCEKCGKIFIKEYQYRSHVSFCKGKITQMATCFECNKMIPAHQEYEHALKYHDIVCPICGVNQMKESKLRNHMKFM
# HKIFNYGKDTQKSDIKNQICVVDQVYYKTCNLCGKVCASFEEFKEHRKEHRTLKQMETAAILEKTKEEEDKAQKSQDQTTPAKPKKEKPNQSSAIECE
# NCEKKFSSRYQLDSHLKRCSAKAVKVLLCDVCELLVPYDEHKEHVKSHEIICDLCGKVCYGKKSFKWHSMHCPAKQNMVKVAKEDLMKTAEDLMKTET
# QRPGKSSINKTKWKKKKTWRSIQLTRNLKRKFTQKQKIFLEKEMGIDTKTLEESQVINSELVSDMIKRGGAPQDSEIEAVKTAIVNEGIENSPKSIKL
# ESENHEEDRFDQDTLEDRDNSERIMSTGDFSDSKTESYPGKGGSQIPVEGDAVECNTRKNGINERRRKRRRRNLSRLGNRRKKARKQKTDQTQEGFVH
# LSNAVMEGKCEEVNANIPRAAGAPFEDSTENEGFSRNTLRTNPTNISRDTSETESDIEEEEVYIGIIQNRKIPTYEPTGNSAMLNLNGMEKTCLDDWL
# IQTSNSHDNAQVWICRHCGKQLGSREEGFDHMISCHPTNKATKEILKEMEMLRLKMLSRSQTDAVLE]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370A22.prfl --predictionStart=0  --predictionEnd=34259  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig1872820180911_busco_2432604931_.temp