# 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..203]--> unknown_A (26) <--[12..86]--> unknown_B (25) <--[0..65]--> unknown_C (62) <--[0..1]--> unknown_D (16) <--[0..4]--> unknown_E (17) <--[0..3]--> unknown_F (26) <--[0..47]--> unknown_G (10) <--[0..5]--> unknown_H (36) <--[3..67]--> unknown_I (18) <--[0..1]--> unknown_J (27) <--[7..29]--> unknown_K (28) <--[20..187]--> unknown_M (29) <--[1..39]--> unknown_N (24) <--[5..11]--> unknown_O (60) <--[3..87]--> unknown_P (84) <--[0..7]--> unknown_Q (23) <--[0..54]--> unknown_R (33) <--[8..33]--> unknown_T (33) <--[0..34]--> unknown_U (25) <--[2..712]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig244420180911_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 = 14007, name = Contig2444) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig2444	AUGUSTUS	gene	3487	5443	0.47	+	.	g1
Contig2444	AUGUSTUS	transcript	3487	5443	0.47	+	.	g1.t1
Contig2444	AUGUSTUS	start_codon	3487	3489	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2444	AUGUSTUS	intron	3738	4120	0.68	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2444	AUGUSTUS	intron	4207	5171	0.65	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig2444	AUGUSTUS	CDS	3487	3737	0.75	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig2444	AUGUSTUS	CDS	4121	4206	0.68	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig2444	AUGUSTUS	CDS	5172	5443	0.75	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig2444	AUGUSTUS	stop_codon	5441	5443	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggggtcgcaccatgaggcgttggtggtaaccccctggaaaaactgtcaattctgttctcttcagtttaagtcgccgc
# gggaattttctcggcatcttagggaatttcattgttccaaagaaggaggttcctacgtttgtcggtttgggcttaataacatatgcccctcgctgcct
# ctagaaggcgtcagtgacatggattatgaaaatcatattgcacgggaccacgtacaggcctcgaaagaaatcaggttgcatgaagatgatttatttat
# ctggtctgctctgaatacacagtccaatattacaccgcatacacatgggagagggttaacgtagactcgagatgacaagtctttagttgtgtcaccac
# caggtgctattccctcagtagttcatgaccagcatcggtggactgtgtttgactccaaagtgaacctccctgctgctctgaatgatcccctgagggtg
# aagagggagacggacttcttcaccaaaacctggggacaagatttctatgagaagttatatgttccagagtcacgctatctcccggaattggacaggag
# atactttgaaaaatataagcacagaatttcaaaggcatga]
# protein sequence = [MGSHHEALVVTPWKNCQFCSLQFKSPREFSRHLREFHCSKEGGSYVCRFGLNNICPSLPLEGVSDMDYENHIARDHVQ
# ASKEIRLHEDDLFIWSALNTQSNITPHTHGRGLTXTRDDKSLVVSPPGAIPSVVHDQHRWTVFDSKVNLPAALNDPLRVKRETDFFTKTWGQDFYEKL
# YVPESRYLPELDRRYFEKYKHRISKA]
# end gene g1
###
# start gene g2
Contig2444	AUGUSTUS	gene	5566	13538	0.24	+	.	g2
Contig2444	AUGUSTUS	transcript	5566	13538	0.24	+	.	g2.t1
Contig2444	AUGUSTUS	start_codon	5566	5568	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	intron	5579	6725	0.38	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	intron	6761	6991	0.85	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	intron	7121	7621	0.99	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	intron	7765	8601	0.99	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	intron	8702	9552	0.98	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	intron	9696	10851	1	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	intron	10979	11296	1	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	intron	11405	12944	1	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	intron	13007	13423	0.79	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	CDS	5566	5578	0.38	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	CDS	6726	6760	0.73	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	CDS	6992	7120	1	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	CDS	7622	7764	1	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	CDS	8602	8701	0.99	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	CDS	9553	9695	0.99	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	CDS	10852	10978	1	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	CDS	11297	11404	1	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	CDS	12945	13006	0.79	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	CDS	13424	13538	0.88	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig2444	AUGUSTUS	stop_codon	13536	13538	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgggtagtgtctagaagaacagagctgaacttcaacagttaccaaagttgttcatgctttcaaactttgacctggaaa
# atacagacacgttcaatgctgtgtttccatggtcacaagtggaggaatgcaagaaaaatggaggctcaccccagtcatctaaactcctgcaggaaaag
# ttgagccattatctagacattgttgaagttcacatagccaaacagatttctaccaagtctgatgccttcttccaggccgtttcatcacacgacatcct
# gcaggactacatgttgattacttgtcagacaattaaacagttgagggataaaatccacagcattgatgagctcttgaccttagggtcattgaagatca
# tgaagttgtcacagacaagagcaaactatgtcaatcttcacaataagctgaagctgatggcgacagtccaccagacccagcccaccatacagctacta
# ctgtccacacaggagtttgtgggggccctagatctcatttccaccacccaggaggtcctcacacaggaactggctggggtacacagcttcagacacct
# gggatcccagctggctgagctagagaacattatagagaagatgttacaggaggattttgggaaatgtgtgtcctctgacctcaatcgtcccatcaccg
# acacggagcatctcctggaagaggagaaagttgtctctcttgtgtttgggatgctcaggaagagccgcttcaactttgtggatgtgtacagagaggaa
# gcattcacagcagtcaaggccattgttaaacagacggttgtggaggctgtgtctgaggcggacaatgtggacagtgaggatggaaatgtcagcagtct
# ggctgaccagatgagaatgctgaactatcctcagtggatgacccttctcaggaaaatcttctctagtttgtcggtgcatctcaacaggacaaaggtga
# ttgcatacatgtga]
# protein sequence = [MGSVXKNRAELQQLPKLFMLSNFDLENTDTFNAVFPWSQVEECKKNGGSPQSSKLLQEKLSHYLDIVEVHIAKQISTK
# SDAFFQAVSSHDILQDYMLITCQTIKQLRDKIHSIDELLTLGSLKIMKLSQTRANYVNLHNKLKLMATVHQTQPTIQLLLSTQEFVGALDLISTTQEV
# LTQELAGVHSFRHLGSQLAELENIIEKMLQEDFGKCVSSDLNRPITDTEHLLEEEKVVSLVFGMLRKSRFNFVDVYREEAFTAVKAIVKQTVVEAVSE
# ADNVDSEDGNVSSLADQMRMLNYPQWMTLLRKIFSSLSVHLNRTKVIAYM]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937029K.prfl --predictionStart=0  --predictionEnd=29696  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig244420180911_busco_2432604931_.temp