# 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..108]--> unknown_A (66) <--[3..5]--> unknown_B (27) <--[2..5]--> unknown_C (47) <--[1..46]--> unknown_D (20) <--[0..5]--> unknown_E (24) <--[0..67]--> unknown_F (21) <--[4..13]--> unknown_G (83) <--[16..40]--> unknown_H (12) <--[6..12]--> unknown_I (23) <--[0..2]--> unknown_J (28) <--[0..44]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2309520180911_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 = 25500, name = Contig23095) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig23095	AUGUSTUS	gene	1	480	0.68	-	.	g1
Contig23095	AUGUSTUS	transcript	1	480	0.68	-	.	g1.t1
Contig23095	AUGUSTUS	intron	174	467	0.68	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig23095	AUGUSTUS	CDS	1	173	0.99	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig23095	AUGUSTUS	CDS	468	480	0.68	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig23095	AUGUSTUS	start_codon	478	480	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgataattacagatatcaacatcagccagccagacatcaatgccagccagccagacatcgacatcagcgtgccagaca
# tcaacaccagccagcctgatatcaacaccagtggagcagagaccagatttgatgagtgcttggtttccctctttactgaccaaccaacaccaaagaaa
# tctccagac]
# protein sequence = [MIITDINISQPDINASQPDIDISVPDINTSQPDINTSGAETRFDECLVSLFTDQPTPKKSPD]
# end gene g1
###
# start gene g2
Contig23095	AUGUSTUS	gene	5868	6581	0.13	-	.	g2
Contig23095	AUGUSTUS	transcript	5868	6581	0.13	-	.	g2.t1
Contig23095	AUGUSTUS	stop_codon	5868	5870	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig23095	AUGUSTUS	intron	6298	6489	0.76	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig23095	AUGUSTUS	CDS	5868	6297	0.26	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig23095	AUGUSTUS	CDS	6490	6581	0.33	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig23095	AUGUSTUS	start_codon	6579	6581	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgccagccgccgacatcgacatcagcgtgccagcatcaacacccagccagcctgatatcaacaccagtggagcagaga
# ccagatttgattaatgtacaccgccagccataacaaccaacttctgccgagacttgacagccttcgtcccttcccatcctcagcagatgaatgacctg
# acctcaccattctacaaagtaccagaagtgcccaagtggagactgaatcgctaccgtgccttcaccagagctccaaccagccatcaaccatcaacaac
# ctacgcaaccagaccatcaaattatcgcagaaggccgttcagctttatggaggcatggtataacagtcactcgaccgcccataccatctccttgatgt
# tccagagatctcgccacaagaggaggaatcaaggaaggggagagggagaaaatggtttctcaaaacaaaggagcaagaaagcaaacgtcatccaggat
# caggaagaagaagaaccgtcgccagtgtcaaccggtgctaaagtaatataa]
# protein sequence = [MPAADIDISVPASTPSQPDINTSGAETRFDXCTPPAITTNFCRDLTAFVPSHPQQMNDLTSPFYKVPEVPKWRLNRYR
# AFTRAPTSHQPSTTYATRPSNYRRRPFSFMEAWYNSHSTAHTISLMFQRSRHKRRNQGRGEGENGFSKQRSKKANVIQDQEEEEPSPVSTGAKVI]
# end gene g2
###
# start gene g3
Contig23095	AUGUSTUS	gene	6786	7100	0.34	-	.	g3
Contig23095	AUGUSTUS	transcript	6786	7100	0.34	-	.	g3.t1
Contig23095	AUGUSTUS	stop_codon	6786	6788	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig23095	AUGUSTUS	CDS	6786	7100	0.34	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig23095	AUGUSTUS	start_codon	7098	7100	.	-	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atggctgatcatccttctttcctccctactgagatcacctttgatacaacgctggaggacatcatcaagaccaccatca
# ttgacgattccccagccacaccccagcctctaaccaccgccagccagcctctcactaccaccagtgatcctgatcatgcttctttcctccctactgag
# atcacctttgacacaacactggaggacatcatcaggaccaccaactctgacgattccccatccacatcccaagctttcaccatctccagccagcctgt
# caccacctccagtattcctgtgccacatccacaatcctga]
# protein sequence = [MADHPSFLPTEITFDTTLEDIIKTTIIDDSPATPQPLTTASQPLTTTSDPDHASFLPTEITFDTTLEDIIRTTNSDDS
# PSTSQAFTISSQPVTTSSIPVPHPQS]
# end gene g3
###
# start gene g4
Contig23095	AUGUSTUS	gene	8638	18232	0.07	+	.	g4
Contig23095	AUGUSTUS	transcript	8638	18232	0.07	+	.	g4.t1
Contig23095	AUGUSTUS	start_codon	8638	8640	.	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	intron	8698	9247	0.86	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	intron	9332	10126	0.99	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	intron	10201	10810	0.66	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	intron	11070	15417	0.36	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	intron	15508	18166	0.2	+	.	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	CDS	8638	8697	0.98	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	CDS	9248	9331	0.95	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	CDS	10127	10200	1	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	CDS	10811	11069	0.62	+	1	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	CDS	15418	15507	0.29	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	CDS	18167	18232	0.32	+	0	transcript_id "g4.t1"; gene_id "g4";
Contig23095	AUGUSTUS	stop_codon	18230	18232	.	+	0	transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atgacgattcaccactacaaacgatccagagcacaggacgaacagctaggattgctagagcaagaacaagctgagcaag
# aaccagaaaagggagaaaacccagaaatctcggataaagaagcattgtttgacggcaaaagtgagtcgaaattctttatcttgaactcgatgggacca
# agaacaaagttagagatatctgagaattcgagatatccaggaacattaaactctgatattcgaaaaccagttagtggaacgttgcatgatatcaatcc
# atatgattttgctatgttcagtgttgacttaactattcaagatattccacatttcaaagaagtcgtcattatggccacaacatgcagcgcctgtggtt
# tcaaagacaatgaagtgaaaggagggtctgggatcgagcccaaagggacaaagatcaccctgaaaataactgacccctcagacatgtccagagatgtc
# ctgaagttggcattatggactacaacttttttaggaaagaatgtcaaacagcttgcaaatgaacctggtattgtttttacctaccacgcaaacgaaat
# cgactgcactacccgctactactgctcaggaggggtggaacagttcaagttctggcctctctaa]
# protein sequence = [MTIHHYKRSRAQDEQLGLLEQEQAEQEPEKGENPEISDKEALFDGKSESKFFILNSMGPRTKLEISENSRYPGTLNSD
# IRKPVSGTLHDINPYDFAMFSVDLTIQDIPHFKEVVIMATTCSACGFKDNEVKGGSGIEPKGTKITLKITDPSDMSRDVLKLALWTTTFLGKNVKQLA
# NEPGIVFTYHANEIDCTTRYYCSGGVEQFKFWPL]
# end gene g4
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CAN.prfl --predictionStart=0  --predictionEnd=31099  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2309520180911_busco_2432604931_.temp