# 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..17]--> unknown_A (12) <--[0..1]--> unknown_B (25) <--[26..39]--> unknown_D (21) <--[4..6]--> unknown_E (38) <--[2..14]--> unknown_F (71) <--[0..32]--> unknown_G (29) <--[0..2]--> unknown_H (25) <--[1..13]--> unknown_I (13) <--[11..29]--> unknown_J (19) <--[2..20]--> unknown_K (26) <--[0..16]--> unknown_L (23) <--[0..3]--> unknown_M (17) <--[0..15]--> unknown_N (15) <--[2..5]--> unknown_O (21) <--[0..1]--> unknown_P (9) <--[0..4]--> unknown_Q (23) <--[26..205]--> unknown_R (30) <--[3..7]--> unknown_S (12) <--[1..15]--> unknown_T (20) <--[0..4]--> unknown_U (6) <--[0..1]--> unknown_V (18) <--[18..130]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig9908320180911_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 = 16387, name = Contig99083) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig99083	AUGUSTUS	gene	6867	8789	0.98	-	.	g1
Contig99083	AUGUSTUS	transcript	6867	8789	0.98	-	.	g1.t1
Contig99083	AUGUSTUS	stop_codon	6867	6869	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig99083	AUGUSTUS	intron	7202	8572	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig99083	AUGUSTUS	CDS	6867	7201	0.99	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig99083	AUGUSTUS	CDS	8573	8789	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig99083	AUGUSTUS	start_codon	8787	8789	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaagtgtgagaaccttttcttgcttactgcactgtgtggcatttggactgtcaacatctcctttgccaagaaagact
# tttacgagattctgggtgtgaagaaaaatgccactgagaagcaaatcaagcgggcttttagaaagcttgctgtacagtatcatcctgacaaaaacaag
# gataaagatgcccaggccaaatttctagaaatagcaaaagcttatgaaaccttaagtgactcagagaagaggaagcgctatgataaattcggtgatga
# atcggacaacgcccaaggcggaggtggtggacatccattcaccttcaacacgaacgactttttccgtggatttgacgaagcattcaacgcccaccgac
# agggccatcaccagcaccaagagggcttctcgttccacttcgggggcaacggtggcaaagacaactcacgattttttaattttgacgatttattcgaa
# gacgatgatgacgacgatgagggcttcttttcctttggggacagtgctttcggcatcatgaagagaatacctttcgactga]
# protein sequence = [MKCENLFLLTALCGIWTVNISFAKKDFYEILGVKKNATEKQIKRAFRKLAVQYHPDKNKDKDAQAKFLEIAKAYETLS
# DSEKRKRYDKFGDESDNAQGGGGGHPFTFNTNDFFRGFDEAFNAHRQGHHQHQEGFSFHFGGNGGKDNSRFFNFDDLFEDDDDDDEGFFSFGDSAFGI
# MKRIPFD]
# end gene g1
###
# start gene g2
Contig99083	AUGUSTUS	gene	10316	15044	0.22	+	.	g2
Contig99083	AUGUSTUS	transcript	10316	15044	0.22	+	.	g2.t1
Contig99083	AUGUSTUS	start_codon	10316	10318	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig99083	AUGUSTUS	intron	10380	12719	0.56	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig99083	AUGUSTUS	intron	12870	13165	0.67	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig99083	AUGUSTUS	intron	13293	14411	0.66	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig99083	AUGUSTUS	intron	14479	14840	0.49	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig99083	AUGUSTUS	CDS	10316	10379	0.58	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig99083	AUGUSTUS	CDS	12720	12869	0.92	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig99083	AUGUSTUS	CDS	13166	13292	0.77	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig99083	AUGUSTUS	CDS	14412	14478	0.51	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig99083	AUGUSTUS	CDS	14841	15044	0.97	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig99083	AUGUSTUS	stop_codon	15042	15044	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggatgaagaagacttgttgccgcttttaggcattggagtgatagaccacggtggcgacgaagattcttcgagtgata
# gtgatgataatgaggatgaagacggtgtttctgctgaagacagcagacggacgagaaggcgagaaccgataacatttgatcagtccctgccagtgtca
# cactctgtaagttattacctaatatggggaatgaaagtatcaataaagtatgatgacttatctcccttgcttgatgacgtcaaaagagaccagcttga
# caaaacagtgtatttgttatcccctcgcaacatgcgaaggggatatagcatcgctgccgtgtgtcctatttgggagatgatttatgtgacgtatttgt
# ttcagtatttgggagatgatttagaagttgtgagctatttgggggatgatttagaggatgtgagaggccgacctttcatgaggagggctctacgattt
# ccatcccagtcatacaaacccggggatggtgctggtgcctggggcagacaattcccctccacctgttccaccaacacacgtgtggccatgctgaaggg
# gtgcatggataaagacaacacatttggggcatcagcatcgtag]
# protein sequence = [MDEEDLLPLLGIGVIDHGGDEDSSSDSDDNEDEDGVSAEDSRRTRRREPITFDQSLPVSHSVSYYLIWGMKVSIKYDD
# LSPLLDDVKRDQLDKTVYLLSPRNMRRGYSIAAVCPIWEMIYVTYLFQYLGDDLEVVSYLGDDLEDVRGRPFMRRALRFPSQSYKPGDGAGAWGRQFP
# STCSTNTRVAMLKGCMDKDNTFGASAS]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937068H.prfl --predictionStart=0  --predictionEnd=28798  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig9908320180911_busco_2432604931_.temp