# 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
# --[10..139]--> unknown_B (56) <--[11..20]--> unknown_D (16) <--[0..1]--> unknown_E (14) <--[0..2]--> unknown_F (28) <--[4..17]--> unknown_G (16) <--[0..1]--> unknown_H (10) <--[0..3]--> unknown_I (15) <--[0..1]--> unknown_J (17) <--[36..105]--> unknown_M (7) <--[0..2]--> unknown_N (12) <--[0..6]--> unknown_O (33) <--[2..21]--> unknown_P (12) <--[0..13]--> unknown_Q (25) <--[0..7]--> unknown_R (34) <--[0..1]--> unknown_S (10) <--[0..2]--> unknown_T (33) <--[2..12]--> unknown_U (11) <--[0..1]--> unknown_V (36) <--[0..1]--> unknown_W (23) <--[6..12]--> unknown_X (32) <--[3..17]--> unknown_Y (41) <--[1..22]--> unknown_Z (15) <--[0..499]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3429220180911_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 = 11609, name = Contig34292) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig34292	AUGUSTUS	gene	1	7567	0.65	+	.	g1
Contig34292	AUGUSTUS	transcript	1	7567	0.65	+	.	g1.t1
Contig34292	AUGUSTUS	intron	1	1496	0.99	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	intron	1649	2000	0.99	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	intron	2131	2352	0.91	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	intron	2489	2604	0.89	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	intron	2712	3096	0.88	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	intron	3229	4306	0.96	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	intron	4377	5633	0.95	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	intron	5763	6055	0.99	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	intron	6233	7087	0.9	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	CDS	1497	1648	1	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	CDS	2001	2130	0.99	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	CDS	2353	2488	0.91	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	CDS	2605	2711	0.83	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	CDS	3097	3228	1	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	CDS	4307	4376	0.94	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	CDS	5634	5762	0.95	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	CDS	6056	6232	0.9	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	CDS	7088	7567	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig34292	AUGUSTUS	stop_codon	7565	7567	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [cctgggcccggcatgctggctgtgggactacttgcggagaagtggacagggtggatatttccttccactaagtggagga
# attgacagttctagcactgcctgtatagtggcatcaatgtgccatctagtggtagaatctgttcagaggggagatgggacctacactccatctgaccc
# ctctgaacttaccggcagactgtttacgacttgttacatgggcacagaaaatagttcagaagacacccgatcaagagctgcagaactggcgggccaga
# ttggaagtttccatttgtctataagcattgatgttgctgtggcagcagtgttaggcgttttcaccacggccttaaaactactgccaaaattcaaagcc
# aacggaggcagtcttagagaaaatctagccttacaaaatgttcaggcccgcttgaggatggttttggcgtacttgtttgcgcagctgtgcttgtgggc
# ccggggaagatctgggggcctcctggtgctggggtccgcaaacgtggacgaggggctgcggggctacatgacgaagtacgactgctccagcgccgacg
# ttaatccgatcggaggaatcagtaaaacagacctccgccgattcattctctactgctcgcaacattttggatacaccgctctcaacaagatcttccat
# gcccctccatcagcagagttagagcccctgcagcagggccagttagcccagacagacgaggaggacatgggtatgacatatgaagaactctctatcta
# tggccgactgagaaaacaaaatggctgtggtccgtacagtatgttctgtaaactggttcaagtgtggaaggacaagttttcacctgaagaggtggcag
# acaaggtgaagcactttttccgctgctatgccattaatcgtcacaaaatgaccacactaaccccgtcataccatgccgagacctacagtccagacgat
# aatcggtacgaccacagacagttcttatacaatgtcaagtggccatggcagttcgaatgcattgatgctcaggtcgagaaactgatgatcctgtacga
# agaatcgcagcgaactcgcggacgaaaccctcccttgtccggttcctctcagaactcagtgaaccataaccagaatgtgtttgaaccttccacccaag
# gtcaaggcacttccgaatacggtattgtcgtatccagccagatctgtgagggggatccaaaggattcggtcaaaacagagaatcatgggagtggacgt
# cagctggacacatcaggtcaaggtcaagctatgaaggtcaagtgtaccgaacaacttggtgatttgacgactaataaggggatcccaagagaagaagc
# ctgtgtctcaccaatgaaagcaacttatagtgaatacagtttagaaaatgagcaagttaagcctgtaatgaatgaaacaaagtcatcaagttctctgt
# ctgtcggatatgagttaatccaggtggataatgctgaggggtgtgaggcggtcttgggataa]
# protein sequence = [LGPACWLWDYLRRSGQGGYFLPLSGGIDSSSTACIVASMCHLVVESVQRGDGTYTPSDPSELTGRLFTTCYMGTENSS
# EDTRSRAAELAGQIGSFHLSISIDVAVAAVLGVFTTALKLLPKFKANGGSLRENLALQNVQARLRMVLAYLFAQLCLWARGRSGGLLVLGSANVDEGL
# RGYMTKYDCSSADVNPIGGISKTDLRRFILYCSQHFGYTALNKIFHAPPSAELEPLQQGQLAQTDEEDMGMTYEELSIYGRLRKQNGCGPYSMFCKLV
# QVWKDKFSPEEVADKVKHFFRCYAINRHKMTTLTPSYHAETYSPDDNRYDHRQFLYNVKWPWQFECIDAQVEKLMILYEESQRTRGRNPPLSGSSQNS
# VNHNQNVFEPSTQGQGTSEYGIVVSSQICEGDPKDSVKTENHGSGRQLDTSGQGQAMKVKCTEQLGDLTTNKGIPREEACVSPMKATYSEYSLENEQV
# KPVMNETKSSSSLSVGYELIQVDNAEGCEAVLG]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093703UX.prfl --predictionStart=0  --predictionEnd=26244  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3429220180911_busco_2432604931_.temp