# 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/Contig4774620180911_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 = 14139, name = Contig47746) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig47746	AUGUSTUS	gene	754	1278	0.53	-	.	g1
Contig47746	AUGUSTUS	transcript	754	1278	0.53	-	.	g1.t1
Contig47746	AUGUSTUS	stop_codon	754	756	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig47746	AUGUSTUS	CDS	754	1278	0.53	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig47746	AUGUSTUS	start_codon	1276	1278	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggaaatggaagcggtttcttctgcagtggacgataattcctttacagtcaacaatgtgcaagtcagatttgattcgg
# agagatgtggtcacttttttcttacaaggagattctgtgaccaaagagatatagaatttaacagaatgtcagagaaatttatattacaaggtgaagat
# gcatctgatcaagaggtatttaaaaacagtaactttctgtgtctacgatcagaacatgtgtgcaaaaaaccagttggaaccaaagctgtttgctccaa
# agaccccaatgataaaatcaattggatccttcatggacagttaactggagttgaaaagatcaaaggtgcgcaacaaccgacagacactgcgcaacccc
# agcagcaaaataatattacaaaaaggagtcgctttaaagtgatgtttaatctgcatcgtgacagcagcaatcccagtgatgcaatgctgtacgatgaa
# aagccatcaatttgctctgtagaaataattctaaaatccgaaacagacacgtaa]
# protein sequence = [MEMEAVSSAVDDNSFTVNNVQVRFDSERCGHFFLTRRFCDQRDIEFNRMSEKFILQGEDASDQEVFKNSNFLCLRSEH
# VCKKPVGTKAVCSKDPNDKINWILHGQLTGVEKIKGAQQPTDTAQPQQQNNITKRSRFKVMFNLHRDSSNPSDAMLYDEKPSICSVEIILKSETDT]
# end gene g1
###
# start gene g2
Contig47746	AUGUSTUS	gene	1473	3386	0.76	-	.	g2
Contig47746	AUGUSTUS	transcript	1473	3386	0.76	-	.	g2.t1
Contig47746	AUGUSTUS	stop_codon	1473	1475	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig47746	AUGUSTUS	CDS	1473	3386	0.76	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig47746	AUGUSTUS	start_codon	3384	3386	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgaaaatagaggaagaccgcttgtctgcactacaaaatcttcgactccaacacaaagtgccaaaatactaccaggaag
# atactgtcaaagagactgaaagaaaagttggtgaatttgaaacagagaaaataaaatgtgacaaaggtagggaagatttgacagctctgcgaattttt
# accattgatcctacaaattccaaagatctcgacgatgcattaagcattgaaagagtaggtgacagctatcgtataggtgttcacatagcagacgttgg
# agctgtcatcagtaaaggtgacgcaatagatttggaggctcaggaaagagcatgtacattttaccccggacaaggcatcaatccctaccatatgttgc
# ctgagccattcggcactaacatatgcagccttcttccaggcgtgccaagaccggcaatcacagttttcttcacgctgaagaaaaaaggaattacggtg
# acaaatgttgaggttaagaaatctaccattttttcatcaaagcaattctcatatgaagaagttcaaaagattattgaagaggataccccagttgatga
# actggccaaggacgttttatgcttgtttaaaatagcaaaaatgcttcgttctattcgcatgcaaaatgccatgttttatttccctgtagaaactaagc
# ttaacggagaacaaaattccgtattgaattcaaaagaagcacactatcttgttgaagaattcatgatactagccaatatgtctatagcacagtatctg
# tggaagatattcccaaacagtttacctgtgcgttgccaggaggctccttcaaaagaaatgatagaaagatggacagagcaaaatagcccaattctaaa
# catggtgctgagattgcagggagttgacccattaaggaataacaatagagtagggctacatcaaatccaagcagcgattagatacaggtatgtcttgc
# catttcagaaatgggtttgggaaaacctttctgggtatataagaggcaatgatatggaaagtgcagctaggctggtttgcacagatgaacttcatcca
# atgcaatgcttggcattggaagagtggatatcttttcaggaaactgccacctatcgatgtagtgggacagcaaaaagggaagaaatgatccacttttc
# tttaaaaatgaacttgtacgttcattttacatcaccgataagaaggtatcctgatctgatcataaatcgactgatccatgcagctttggagaataccg
# agtgcccatattcagcacaggaagtagatgcgctctgtgaaggatttaacagcacaatgcgtagagcaaaacaattccaaaaacaatgtcaacttatg
# ttttgggggtttaagttgaaaaagacaccacagattctgcatggctttgtgagagacttttcagaaaagtctatttcaatagtaatacctgggttaag
# atcactgcccatgtattgtaaagagattccactcaatttactccagttgagcgaaaaacctattttatcaagggaacaagatccaaaagatgaactta
# tggttctgaagtggttgcaaagactttatgatgttactggaaaacctatcagaagggaaggatggttatcacctgaagctagagcaaagttttgcaaa
# caactaaatccacacacaagagcaaagtttataactcaggaatcttggaaaactgttctgaaaatggtcatagaggggaatctcgtcggtctcagtcg
# gttgactgagaaacaaaaagaagatacatttggtttagatgaagataaacatggctttgtagatacttgtaaaaatacagttcttgatcactcatcag
# gaggggagagtgtcccgaatgttatcaaacaaggatgcgagtacagcatgtcttttcccgtggacaaatag]
# protein sequence = [MKIEEDRLSALQNLRLQHKVPKYYQEDTVKETERKVGEFETEKIKCDKGREDLTALRIFTIDPTNSKDLDDALSIERV
# GDSYRIGVHIADVGAVISKGDAIDLEAQERACTFYPGQGINPYHMLPEPFGTNICSLLPGVPRPAITVFFTLKKKGITVTNVEVKKSTIFSSKQFSYE
# EVQKIIEEDTPVDELAKDVLCLFKIAKMLRSIRMQNAMFYFPVETKLNGEQNSVLNSKEAHYLVEEFMILANMSIAQYLWKIFPNSLPVRCQEAPSKE
# MIERWTEQNSPILNMVLRLQGVDPLRNNNRVGLHQIQAAIRYRYVLPFQKWVWENLSGYIRGNDMESAARLVCTDELHPMQCLALEEWISFQETATYR
# CSGTAKREEMIHFSLKMNLYVHFTSPIRRYPDLIINRLIHAALENTECPYSAQEVDALCEGFNSTMRRAKQFQKQCQLMFWGFKLKKTPQILHGFVRD
# FSEKSISIVIPGLRSLPMYCKEIPLNLLQLSEKPILSREQDPKDELMVLKWLQRLYDVTGKPIRREGWLSPEARAKFCKQLNPHTRAKFITQESWKTV
# LKMVIEGNLVGLSRLTEKQKEDTFGLDEDKHGFVDTCKNTVLDHSSGGESVPNVIKQGCEYSMSFPVDK]
# end gene g2
###
# start gene g3
Contig47746	AUGUSTUS	gene	3791	5314	0.3	-	.	g3
Contig47746	AUGUSTUS	transcript	3791	5314	0.3	-	.	g3.t1
Contig47746	AUGUSTUS	stop_codon	3791	3793	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig47746	AUGUSTUS	intron	4452	5249	0.36	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig47746	AUGUSTUS	CDS	3791	4451	0.4	-	1	transcript_id "g3.t1"; gene_id "g3";
Contig47746	AUGUSTUS	CDS	5250	5314	0.32	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig47746	AUGUSTUS	start_codon	5312	5314	.	-	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgacagaggcaaccattctagtccgaggcaaaacaaaatcacatatcatactcttttgggtaagcaacaacgcaataa
# acttagcattcacaacagcaaagtatggtaattccagaccttcatccctctcacggcggaggagttctgtatcagagtcattatcttcctgtcaagtt
# agtgaattcaaccactctgatagcgatgatgtggacacgggttctgattctgaattggaattcgaaactcatgacccacctgcacttgaactttctgg
# ggaaggcgagaacgcctttgatgaaaccgaggacgaattcactacttctagatttcaagaaagtcaaaagctttattctagcgatgaaaatgagcaat
# gtagaatcctagagcaagatattatgcagaatggcttgcatctttcaaatgcatatgatatcgaagacaagaaagagaagaagcgattttatgatgaa
# atgattccaacagagaacctagaaaaactattaagatccaatccacatcagtataaacgctgtgtgttcagggttgaaagttctcacgaatccatctg
# caaggttctcgaccaacccgacgtagatggtgtggaggaaattcaaatatcaggaagatcgaaagctggaaaagcttttgatacggacatnaggaaat
# tcaaatatcaggaagatcgaaagcagggaaagcttttgatatggacactgttttggtag]
# protein sequence = [MTEATILVRGKTKSHIILFWVSNNAINLAFTTAKYGNSRPSSLSRRRSSVSESLSSCQVSEFNHSDSDDVDTGSDSEL
# EFETHDPPALELSGEGENAFDETEDEFTTSRFQESQKLYSSDENEQCRILEQDIMQNGLHLSNAYDIEDKKEKKRFYDEMIPTENLEKLLRSNPHQYK
# RCVFRVESSHESICKVLDQPDVDGVEEIQISGRSKAGKAFDTDXRKFKYQEDRKQGKLLIWTLFW]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CAV.prfl --predictionStart=0  --predictionEnd=23311  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4774620180911_busco_2432604931_.temp