# 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..317]--> unknown_A (10) <--[0..15]--> unknown_B (32) <--[4..9]--> unknown_C (111) <--[0..51]--> unknown_D (52) <--[2..14]--> unknown_E (40) <--[0..2]--> unknown_F (69) <--[2..39]--> unknown_G (23) <--[0..45]--> unknown_H (20) <--[0..4]--> unknown_I (68) <--[0..4]--> unknown_J (12) <--[0..19]--> unknown_K (15) <--[0..1]--> unknown_L (15) <--[0..2]--> unknown_M (12) <--[0..7]--> unknown_N (29) <--[0..20]--> unknown_O (15) <--[17..63]--> unknown_Q (43) <--[0..117]--> unknown_R (32) <--[19..383]--> unknown_S (29) <--[35..83]--> unknown_U (19) <--[0..1]--> unknown_V (15) <--[7..55]--> unknown_W (13) <--[10..19]--> unknown_Y (13) <--[1..15]--> unknown_Z (17) <--[0..50]--> unknown_AA (16) <--[0..1]--> unknown_AB (36) <--[0..40]--> unknown_AC (26) <--[5..7]--> unknown_AD (11) <--[1..12]--> unknown_AE (26) <--[2..13]--> unknown_AF (21) <--[16..182]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3671320180911_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 = 18281, name = Contig36713) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig36713	AUGUSTUS	gene	6492	8542	0.69	+	.	g1
Contig36713	AUGUSTUS	transcript	6492	8542	0.69	+	.	g1.t1
Contig36713	AUGUSTUS	start_codon	6492	6494	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig36713	AUGUSTUS	intron	6990	7357	0.7	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig36713	AUGUSTUS	CDS	6492	6989	0.71	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig36713	AUGUSTUS	CDS	7358	8542	0.76	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig36713	AUGUSTUS	stop_codon	8540	8542	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggaggacatttcccgtgtatcagaagtcctgtacgtgggtctctgtcgtaaaatagggacaccgatagaagtgacca
# tcagaagggacgtgagagacatgaaggaaatgatagctaaacctgtagagatatatagagaagagagaaggatgttaagtggtagctatagggaggga
# ttcaggtttaaatcatcggacatggactggatgttgtggttatgtaaccataagctgataactgatatctcccaggccaggctttacgatagaacaaa
# acacaccattatactgatggaggacaatgatacaccgcctggatttgtcaaactacagcttctgacatctccacgagataacgacatcgcatcatcag
# ctgttccagtcaatgacagagtctacatctccagtttactgtggcaacaacacacgtttgaagcagttaatgctgccaacagttcccagagagtcact
# agtcacggtccctgtgctaatgggtttgcggggtctgttgagtggtgccctaactatttactgaattgtttctggaagtgtttcaaatacctcattga
# ctgtgtttatagcggcgtgttcccctattttttcattccgcagtacaatatgtttatcaacaaagtgacgggtagtccaggcgttgctcgctatgaac
# agctttatcagtattacagaatgggcgtgtcctgtctgctgcttagcccaaccctcagctcaatcctagaaccagccctcagcagtccaacatttagt
# attccctctgccgaaggacatatcaaaactgtggcggatatcgatacggttatctacagtgaaattccgcctctcggtcaggatttcaaaagtcctag
# ttgtcatttcatagttttgatgacattagaaagattaacacggttatcacattcaccctacaaaacattagcattgcaacattatacagcgggtgttc
# tcatccacacggccttcatgatagctaacaatatttcataccacacacatagaaacttgtatacatcagacaaaattgtctgtaacattctgaaactg
# gcatcaagggtaggtcctgtgtccgattcactgtatctcgccttgtattactatagaacaggtagatacaatgaagcactccgtgtcacttatctcac
# taaacaaagactatcacagccctttatcatgtattacaatgatgtagacagacatagatacagtgaggctgtaggtagtcggtctctgtctaggagaa
# tgaaaacagcctgggtacgcgatgtgaagttgtacattgaagtccactatattgatgaattaatgttagaacaggaagtgagtaaacaaaacggtgta
# cctctcttatacattcccccgtttgtgttgacagacatgctattggtgttatctcactacagactaggtaacagatcccagtatctacagtcactgac
# agacctacagaccctgctgatctatgatgatggtagatatgtaccgttacgttacagggacctgtcgtggcagatactggggatctgtcagcatgttg
# tgggggacttacacggggcgttacactcttatcaagagtcacttagacaaaaacaatctcagaaaatacagacagctacagaaaatagaatagcgttt
# gttgaacgtcaactacacagaaatacatccttataa]
# protein sequence = [MEDISRVSEVLYVGLCRKIGTPIEVTIRRDVRDMKEMIAKPVEIYREERRMLSGSYREGFRFKSSDMDWMLWLCNHKL
# ITDISQARLYDRTKHTIILMEDNDTPPGFVKLQLLTSPRDNDIASSAVPVNDRVYISSLLWQQHTFEAVNAANSSQRVTSHGPCANGFAGSVEWCPNY
# LLNCFWKCFKYLIDCVYSGVFPYFFIPQYNMFINKVTGSPGVARYEQLYQYYRMGVSCLLLSPTLSSILEPALSSPTFSIPSAEGHIKTVADIDTVIY
# SEIPPLGQDFKSPSCHFIVLMTLERLTRLSHSPYKTLALQHYTAGVLIHTAFMIANNISYHTHRNLYTSDKIVCNILKLASRVGPVSDSLYLALYYYR
# TGRYNEALRVTYLTKQRLSQPFIMYYNDVDRHRYSEAVGSRSLSRRMKTAWVRDVKLYIEVHYIDELMLEQEVSKQNGVPLLYIPPFVLTDMLLVLSH
# YRLGNRSQYLQSLTDLQTLLIYDDGRYVPLRYRDLSWQILGICQHVVGDLHGALHSYQESLRQKQSQKIQTATENRIAFVERQLHRNTSL]
# end gene g1
###
# start gene g2
Contig36713	AUGUSTUS	gene	10540	18281	0.03	-	.	g2
Contig36713	AUGUSTUS	transcript	10540	18281	0.03	-	.	g2.t1
Contig36713	AUGUSTUS	stop_codon	10540	10542	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	intron	10670	14368	0.26	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	intron	14570	14753	0.33	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	intron	14782	15689	0.37	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	intron	15706	15928	0.56	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	intron	15947	16914	0.49	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	intron	17041	18281	0.33	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	CDS	10540	10669	0.69	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	CDS	14369	14569	0.27	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	CDS	14754	14781	0.55	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	CDS	15690	15705	0.72	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	CDS	15929	15946	0.55	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig36713	AUGUSTUS	CDS	16915	17040	0.45	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [gccaagcctgggacctgccctggacatttgcgctgcgacagtttacctaccttgctggaagacgagaacgcccagtttc
# accacagtcctttttctttcaacagagcagctggacgcgcctttcagagtctgccttattacactgtgtttgttgagtcaggagcaggtaaagccaga
# cgcataaacaggccagcggaaacagtgaaaaataggagacacttcggatgtggaccccgcactaacacacgagatatatggcacactattgagggaca
# tggccatagtacatcacacctcagtgaactatttctgttcggcacagacgaccaaggcactgcgctgctacctcccactactcgttactcagcaaaca
# agtatccacgcctgagccctgattcaaagagcactatggtcacggtgagatgtagactgtcgtcacgggctgctcactcctcgaaagaactagacaga
# agttccagtggtggcccaacgtcctatgttgtagagttttccatttga]
# protein sequence = [AKPGTCPGHLRCDSLPTLLEDENAQFHHSPFSFNRAAGRAFQSLPYYTVFVESGAGKARRINRPAETVKNRRHFGCGP
# RTNTRDIWHTIEGHGHSTSHLSELFLFGTDDQGTALLPPTTRYSANKYPRLSPDSKSTMVTVRCRLSSRAAHSSKELDRSSSGGPTSYVVEFSI]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093700N7.prfl --predictionStart=0  --predictionEnd=38263  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3671320180911_busco_2432604931_.temp