# 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
# --[14..135]--> unknown_A (11) <--[0..9]--> unknown_B (16) <--[2..36]--> unknown_C (17) <--[1..61]--> unknown_D (18) <--[0..8]--> unknown_E (17) <--[2..12]--> unknown_F (28) <--[0..26]--> unknown_G (21) <--[0..11]--> unknown_H (27) <--[15..45]--> unknown_I (38) <--[8..83]--> unknown_J (16) <--[5..25]--> unknown_K (11) <--[10..27]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig9181320180911_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 = 7595, name = Contig91813) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig91813	AUGUSTUS	gene	1	4014	0.19	+	.	g1
Contig91813	AUGUSTUS	transcript	1	4014	0.19	+	.	g1.t1
Contig91813	AUGUSTUS	intron	1	561	0.63	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig91813	AUGUSTUS	intron	572	1899	0.39	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig91813	AUGUSTUS	CDS	562	571	0.39	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig91813	AUGUSTUS	CDS	1900	4014	0.51	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig91813	AUGUSTUS	stop_codon	4012	4014	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [cttcaggcaggttaaaactcttaaatatggagaggatgatgatgtcaaacaagccatgcaaaaggcagatgaaatcatt
# gcgataaaccaagcacagctaaatgagaaactttctgaattaccgggagaggagccgttgctaaagactaagactggctttagtaaaacactaattaa
# taagtctccctccacagcccaagatcccaatgttccgcatacaatgacctcaccagatcaacaggggttcatggctgcaatggaagcagatgccagag
# agagagcagagagaagacaagctggtgaggcgaaagccaatgagttaaaagagaaaggcaatgaggaattcagacgaggaaattatgagaaggcgttg
# gagttttactcagaaggactgactcatctcaaagatcatcttgctctttggaccaacaaagcccaaacaaatatcaaattgggtaggtttgaggaagc
# tctcatagactgtgactgggccacaagggttttcagtaacagcatgaaagcttatgttctaatgggaaaggcttatcttggactcagaaaatacgaaa
# aagcaagagtggcgtacaagaaagcccttgaatgtgacccaaccaaacaaaatcttatcaaagactatttagcggatgttgatagagtagagaggacc
# cagcaggaagaagaaaaagcaaaagaggcatttcaggctggagaaaagggccctgttgctttacttcaacaattagcgaaaaaagatcaacttccaat
# tttttacagtggaggatttcaagttctgcaaaatttcctgaagaacaatgaacagaaaacacttttccgaacagagggaggatttcaaatcattactg
# agcatccatgcttctcaaaatgtttctcggcttctccaaggagtttgtccaaagaagaacttgatatgttgaaatctggcatggacatgttcagtttg
# gcttgtgaagataatgaaaagaatcaggaaattttcttacaaatagaaggaatgcccaacaaactaatgaggttcatggaagtgaaaattaaaggtcc
# tggtcgtggtctgaaatccagttgtgtgaagatattacacactgtgacaatatctgtgattggacgatcgttagttcttcaaaagtttgacattccac
# ggttaatgaccattgtgttcaatttaattcgaacaaatgatgattctgcattaacttcgggatgtgttctaaacaatctggctcttgacaacaagttt
# aagcaacagttaagagacaaaatcgaaattgatgttctgccagcatttgaaaatgttctaaaagaaggatccagcaaccaatctgttctacctacctg
# tgtgtccacaatcaccaacctctccaatgatgttgttatcaggaaaaagttgtctgatcgcaaagatctctggaagattcttgtggatgccattacca
# gacacaaagaaaagctgccgcagcctctcagtgtagagctcgttgaagcttgtttgggcctcatttctaatttgacacacgaaggaactagtataaac
# tttaaagagttcagccttcccatttgcaagcaatgtctgatgatctgtcagtctctgaagcactacaagttgatggtatctcgcagtctcgggatcct
# aagccatatcttaccctactccattccttccgtggactggttctgtgacaatgaaggagtagaggtcctaatgtacattctcaagaatgatgaagatt
# cagcaaataggaagtgtgccttgaaggccctcactggttgttcacagattaatgagcatgctagagtcttcattgtggaccacaaagggctggggact
# ctcattaaacagctgaagagtgacgatgaaacagtcattgggaacgctgcactttgtctcagtcactgcacccaggtcccgaaagtgtgcgcagcttt
# atcaaagacagatattataaaagaccttttggttctggctcgtgatggaaacaagtccggtctccagcagaattgtgccattcttatagctaagcttg
# ctcagggtgataagcgacatttagagagactgagggaactccatggtattgacattcttcacgactgtatgaagtatttgaagtga]
# protein sequence = [FRQVKTLKYGEDDDVKQAMQKADEIIAINQAQLNEKLSELPGEEPLLKTKTGFSKTLINKSPSTAQDPNVPHTMTSPD
# QQGFMAAMEADARERAERRQAGEAKANELKEKGNEEFRRGNYEKALEFYSEGLTHLKDHLALWTNKAQTNIKLGRFEEALIDCDWATRVFSNSMKAYV
# LMGKAYLGLRKYEKARVAYKKALECDPTKQNLIKDYLADVDRVERTQQEEEKAKEAFQAGEKGPVALLQQLAKKDQLPIFYSGGFQVLQNFLKNNEQK
# TLFRTEGGFQIITEHPCFSKCFSASPRSLSKEELDMLKSGMDMFSLACEDNEKNQEIFLQIEGMPNKLMRFMEVKIKGPGRGLKSSCVKILHTVTISV
# IGRSLVLQKFDIPRLMTIVFNLIRTNDDSALTSGCVLNNLALDNKFKQQLRDKIEIDVLPAFENVLKEGSSNQSVLPTCVSTITNLSNDVVIRKKLSD
# RKDLWKILVDAITRHKEKLPQPLSVELVEACLGLISNLTHEGTSINFKEFSLPICKQCLMICQSLKHYKLMVSRSLGILSHILPYSIPSVDWFCDNEG
# VEVLMYILKNDEDSANRKCALKALTGCSQINEHARVFIVDHKGLGTLIKQLKSDDETVIGNAALCLSHCTQVPKVCAALSKTDIIKDLLVLARDGNKS
# GLQQNCAILIAKLAQGDKRHLERLRELHGIDILHDCMKYLK]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370TFO.prfl --predictionStart=0  --predictionEnd=22559  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig9181320180911_busco_2432604931_.temp