# 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
# --[2..905]--> unknown_A (8) <--[1..2]--> unknown_B (20) <--[0..453]--> unknown_C (22) <--[8..49]--> unknown_E (23) <--[4..17]--> unknown_F (18) <--[0..5]--> unknown_G (28) <--[18..40]--> unknown_J (9) <--[8..12]--> unknown_K (17) <--[0..6]--> unknown_L (22) <--[0..6]--> unknown_M (9) <--[0..3]--> unknown_N (10) <--[0..1]--> unknown_O (23) <--[4..7]--> unknown_P (29) <--[0..24]--> unknown_Q (21) <--[4..6]--> unknown_R (11) <--[1..3]--> unknown_S (86) <--[0..46]--> unknown_T (26) <--[0..2]--> unknown_U (40) <--[2..57]--> unknown_V (38) <--[1..7]--> unknown_W (14) <--[0..2]--> unknown_X (22) <--[3..13]--> unknown_Y (13) <--[4..161]--> unknown_Z (20) <--[2..64]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6716320180911_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 = 20042, name = Contig67163) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig67163	AUGUSTUS	gene	1	6780	0.52	+	.	g1
Contig67163	AUGUSTUS	transcript	1	6780	0.52	+	.	g1.t1
Contig67163	AUGUSTUS	intron	1	3028	0.55	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig67163	AUGUSTUS	CDS	3029	6780	0.57	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig67163	AUGUSTUS	stop_codon	6778	6780	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [aattccccagagaagaacatacaccaagcataaatgatgaacaaaatttacaaaggtccgatagtgttccgaacatttc
# ttgcaatgcgtcaatcattccggggcgttccttctcctcattatttcaaccatcgcatgcgcagtcctgttcagatatttccgttcaagttgataatg
# tgaacaatgaaagtgacgatgtttctactgatgtggaagaacttgagtcatgcagcgacaaaaccgaattggaggacggagactttgagacagacaac
# gaagacttagatgattttcagtcccagcgtagttttgtgattccacaagaagacagcgaaaaatctaaatttgaagaaagttgtgctaattatgaaaa
# cgaagaaaatgaggatgagaatttactgcttcaagatatgatgaaatatggtttagacttacccgaatgtagcgaaaatgataagaagcagaagtttt
# atgacgaatttttgccagttgaccagttagaaacgagacttcggtcaaatacacagcgttacaaacgttgcaaagtttccattcaaggagcgcacata
# gcgcggtgtttcaaccttgacattcgggatgagctccaagaaattgaaatatcaggaagatccaaggcaggaaaagtatttgatggcgacgtagtgtt
# agtagagatatttaactatgaaaaatttacaaaaactgtcattcagaggttacagaaagacatcaataaagacaaccgttcgcagagaatttatggca
# aaattattggagtttttgaaagaaacaaagcaagagatattgatcaccctgtgttcgtttgtactttggacgacaccgcaaatcacctgatgcgacct
# gtctgtaaaacggttccaaaacttcatcttgatcatgacaaacggaaaaagtacatcattcaggtgtacaaatacaatacaaggtcatcaaatattga
# accaaactatgaatttcgaatcgaccccggtagaaagtcaagctttgtgtttttggttgtttacctgtcttggtccggcttgtatccgatgggtgctg
# tgatagatgttattgaggttgaggaaagtttctcatctgcaatgaaaatccttcgacttcaccatcaagtgccacaatattatcagaaagaaacggtt
# gagtatacaaagaaactacttgatgaattggaatcaaacgaaatcacgagcgaagataatcgcaaggatctttctcatcttagggtctttactattga
# cccagaaggatctcaagaccttgatgatgctatcagcatagaggaagtagatggcatgtttgaaataggagttcatatttctgatgtaacatttgtag
# tgaagaaagatgaccaacttgacttagaagccaaagaaagagcttgtacattttatcctggccaaggaatgaatccttaccatatgctccctgaacca
# ctgtcacgcaatatctgtagtttaattccaggagtaatgcgacctacattgtctgtcatatacagaatgacaaaaaacggacacgtggaaaatcaacg
# tttgcaaaaatccacagttaaatcttgtaggaaatttacatatgaggaagtgcaaaaaataatagagagaaaatctgcagagagtgccttggaagaag
# atatacttcaactctttgagatagcaaaaacaatacggaaaaaaagacctggggcaggtttttactcctttcccgtggaggtgaaattaaatgacagc
# ggagactcaatactaaattcaagagaagctcattatcttgttgaagagttcatggtattagcgaatacaacggttgctgcatatctatatagccgatt
# tccgaaagcgatgccccttcgttgtcaacctgcaccatcatttgaaattctcaagaagtggagagaccaaaatcatcctttctttcacatggtgcttc
# gccttcaaaatattgatccaagtgcaggaattggtagtgagaagattgatctgaattctcttacacctcttagatatacaaggatcatgcctgtccaa
# aaatgggtctgggaaaatattctcgatgcactaaagaaaggtgatatccagtcagcaattcaatatatatgtactgacgaactgcaccccagccaatg
# tttggcgttagaggagtggatatctttccaggaaagtgcttcgtacagatgtagtgggacgttaaatgagccaagggaaggaatgcacttttcattgc
# agcgaacgatgtatgtacattttacatcaccaataagaagatatccagacattattgttcatcgtcttcttcatgctgcaatagataatcaaaaatgt
# ccatattcagaatctgaggttgacacgctatgccaaaacttgaacgatgtcattagcagagcaaaggctttccaaaaagaatgtagaatgctgatctg
# ggggtttagattaaagcaatccccacagatactacaaggatttattagagaagtgtccgacagagctgtatctttggttttgcctggactccgaactc
# ttcctcatttttgcaaagaatttgaactgaatcttcttcacgtatatgagaggccgaaatttgataaagatacgacaactggagaaatcataatgaca
# ctgaattggctattgcgcgtgtatgatgtgtcagggaagccaaacagagacgagcgtatggagcagagattgcactggttgtcagaagaagcgaggaa
# agaagtctgtaaacgaataaatcctcacactagaacaaaatttgtgcaacaggagcattggaaagattatcttaagttagttcttaaaggggagcctc
# aggatctaaaaaaatatattttgcaacagcaaaatacaacaaaatctaaaaacaaaaaagatatggatgaagatcttcacaactatgtgccagcctgt
# aaggatacaatattagatcattcgtctgaagtagaagacggagaagtgattcgtcaagcatgtcgattttctatgtctttttctcgaggacaagtact
# ttgtgtgcaaattacagctgaaccacagaaaggggtccttgttccatccttgcagttgcttgatatgacaaagaacataaagcactgcatgcaacaca
# gtcgcgatcctattaagtttttgtcgaaatattcaatacacaaatcaaagggaaaatatccttcagctaccgattatctgcatatttggttaccaata
# attgaaatggaagcggtcacaaatgcagttcatggtgattctccgattattaacggagtggaaattttcatggagtcaccaaacaggggacatttcat
# tcttacttattatttctgtgaacaaagggacattgattttagtacaatatctccacatttcattcttgtcggtaacgaagataacaaaaatgaaatca
# ttacaaactcggatttcctatgtattagatcggaacattctttcgataactctaacgaagaaaggaaaccgtctgctgttgacccgaataacagattt
# cagtgggtccttcacggaaaaatagaccatatagagagaatgatgaaatccaaacccaaacaaaatgaagcagaggaattgagagaaaaggtcaatga
# aaagaagcgaactgttattgataagtacaaagtccatttcaaacttcacagggaaagcaacgaagcaatgaccgagatgtcatccatggaaaatggat
# accctagctgcatagaaatggtgcaaaaatcagaaactgaaacgtaa]
# protein sequence = [FPREEHTPSINDEQNLQRSDSVPNISCNASIIPGRSFSSLFQPSHAQSCSDISVQVDNVNNESDDVSTDVEELESCSD
# KTELEDGDFETDNEDLDDFQSQRSFVIPQEDSEKSKFEESCANYENEENEDENLLLQDMMKYGLDLPECSENDKKQKFYDEFLPVDQLETRLRSNTQR
# YKRCKVSIQGAHIARCFNLDIRDELQEIEISGRSKAGKVFDGDVVLVEIFNYEKFTKTVIQRLQKDINKDNRSQRIYGKIIGVFERNKARDIDHPVFV
# CTLDDTANHLMRPVCKTVPKLHLDHDKRKKYIIQVYKYNTRSSNIEPNYEFRIDPGRKSSFVFLVVYLSWSGLYPMGAVIDVIEVEESFSSAMKILRL
# HHQVPQYYQKETVEYTKKLLDELESNEITSEDNRKDLSHLRVFTIDPEGSQDLDDAISIEEVDGMFEIGVHISDVTFVVKKDDQLDLEAKERACTFYP
# GQGMNPYHMLPEPLSRNICSLIPGVMRPTLSVIYRMTKNGHVENQRLQKSTVKSCRKFTYEEVQKIIERKSAESALEEDILQLFEIAKTIRKKRPGAG
# FYSFPVEVKLNDSGDSILNSREAHYLVEEFMVLANTTVAAYLYSRFPKAMPLRCQPAPSFEILKKWRDQNHPFFHMVLRLQNIDPSAGIGSEKIDLNS
# LTPLRYTRIMPVQKWVWENILDALKKGDIQSAIQYICTDELHPSQCLALEEWISFQESASYRCSGTLNEPREGMHFSLQRTMYVHFTSPIRRYPDIIV
# HRLLHAAIDNQKCPYSESEVDTLCQNLNDVISRAKAFQKECRMLIWGFRLKQSPQILQGFIREVSDRAVSLVLPGLRTLPHFCKEFELNLLHVYERPK
# FDKDTTTGEIIMTLNWLLRVYDVSGKPNRDERMEQRLHWLSEEARKEVCKRINPHTRTKFVQQEHWKDYLKLVLKGEPQDLKKYILQQQNTTKSKNKK
# DMDEDLHNYVPACKDTILDHSSEVEDGEVIRQACRFSMSFSRGQVLCVQITAEPQKGVLVPSLQLLDMTKNIKHCMQHSRDPIKFLSKYSIHKSKGKY
# PSATDYLHIWLPIIEMEAVTNAVHGDSPIINGVEIFMESPNRGHFILTYYFCEQRDIDFSTISPHFILVGNEDNKNEIITNSDFLCIRSEHSFDNSNE
# ERKPSAVDPNNRFQWVLHGKIDHIERMMKSKPKQNEAEELREKVNEKKRTVIDKYKVHFKLHRESNEAMTEMSSMENGYPSCIEMVQKSETET]
# end gene g1
###
# start gene g2
Contig67163	AUGUSTUS	gene	11661	17459	0.09	+	.	g2
Contig67163	AUGUSTUS	transcript	11661	17459	0.09	+	.	g2.t1
Contig67163	AUGUSTUS	start_codon	11661	11663	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig67163	AUGUSTUS	intron	11722	13573	0.59	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig67163	AUGUSTUS	intron	13750	15019	0.62	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig67163	AUGUSTUS	intron	15131	17351	0.15	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig67163	AUGUSTUS	CDS	11661	11721	0.67	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig67163	AUGUSTUS	CDS	13574	13749	0.85	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig67163	AUGUSTUS	CDS	15020	15130	0.63	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig67163	AUGUSTUS	CDS	17352	17459	0.35	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig67163	AUGUSTUS	stop_codon	17457	17459	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggaacatcggcaagtcgttttttgcggtccaaataataaatctgtggatctagttgcaaaggcagaaagcattgcac
# catgtgtagaaccaaggcaaacaggttgtcttataggagatcaacaacagcttagggccctgttcacagtcacgatgctgctgaatgggtctaaacgt
# atcattggtttaacagttattcgaaaactggcacaacatgctgcggttcctagtaggatgacatccatcaacatcatgtcgcagtacaatgcacagtt
# gcacgaggatccgaaaagcaactactggaccggaaaacgtaatatcaacgtcacactgttgtacgctatcaggttccgtctagatttgacaacggata
# atcccgtttacgttgttcaacctaaaggcgattcacggtgggttgtgaccgtcagcgaggatgctactctacatggcacctga]
# protein sequence = [MEHRQVVFCGPNNKSVDLVAKAESIAPCVEPRQTGCLIGDQQQLRALFTVTMLLNGSKRIIGLTVIRKLAQHAAVPSR
# MTSINIMSQYNAQLHEDPKSNYWTGKRNINVTLLYAIRFRLDLTTDNPVYVVQPKGDSRWVVTVSEDATLHGT]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CAV.prfl --predictionStart=0  --predictionEnd=25361  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6716320180911_busco_2432604931_.temp