# 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..49]--> unknown_A (8) <--[18..47]--> unknown_B (13) <--[2..15]--> unknown_C (28) <--[1..22]--> unknown_D (21) <--[36..147]--> unknown_G (16) <--[29..155]--> unknown_H (43) <--[12..51]--> unknown_J (14) <--[2..5]--> unknown_K (24) <--[0..4]--> unknown_L (8) <--[0..12]--> unknown_M (13) <--[0..2]--> unknown_N (12) <--[4..22]--> unknown_O (23) <--[0..62]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2992620180911_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 = 11889, name = Contig29926) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig29926	AUGUSTUS	gene	1	4668	0.08	+	.	g1
Contig29926	AUGUSTUS	transcript	1	4668	0.08	+	.	g1.t1
Contig29926	AUGUSTUS	intron	1	636	0.89	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29926	AUGUSTUS	intron	817	2065	0.81	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29926	AUGUSTUS	intron	2154	3433	0.51	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29926	AUGUSTUS	intron	3550	3691	0.7	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29926	AUGUSTUS	intron	3834	4631	0.22	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29926	AUGUSTUS	CDS	637	816	0.89	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig29926	AUGUSTUS	CDS	2066	2153	0.79	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig29926	AUGUSTUS	CDS	3434	3549	0.68	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig29926	AUGUSTUS	CDS	3692	3833	0.86	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig29926	AUGUSTUS	CDS	4632	4668	0.22	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig29926	AUGUSTUS	stop_codon	4666	4668	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [agactggagaatttcagattgatacaaacagatcttaccacggtatgaccctaaagtttgtgacagagggtgggccatc
# acagaaaaaacgccccgagccacagagacaacaaccacaaccactacagccaatgtcacgaccggtatcacaggccagacctccccccagtcagaaaa
# aaggttccagaactcccatcatcattatcccagcagcaacaacatcactaatcacaatgttcaacgcaaaagacatactacaagatctgagattgtac
# ctgccatatttttctagggaacgagttgttgcagtgtttgtgcagggtcctgcatggcagtttaaaaactggccttggagtggaaaccctgtggaaat
# attttccaaagtgaaggcctttcacttaaagtggggagaacttcctttggaacccaatgtacagaaatgggcggtgacagtgctaaatcttgacagga
# tgaggcgacatcttgacagagcaacactcaatacgttctgggaagtgctggacaaatacatggcaaaggataaacctcatctgagatactag]
# protein sequence = [TGEFQIDTNRSYHGMTLKFVTEGGPSQKKRPEPQRQQPQPLQPMSRPVSQARPPPSQKKGSRTPIIIIPAATTSLITM
# FNAKDILQDLRLYLPYFSRERVVAVFVQGPAWQFKNWPWSGNPVEIFSKVKAFHLKWGELPLEPNVQKWAVTVLNLDRMRRHLDRATLNTFWEVLDKY
# MAKDKPHLRY]
# end gene g1
###
# start gene g2
Contig29926	AUGUSTUS	gene	9226	11889	0.33	-	.	g2
Contig29926	AUGUSTUS	transcript	9226	11889	0.33	-	.	g2.t1
Contig29926	AUGUSTUS	stop_codon	9226	9228	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig29926	AUGUSTUS	intron	9450	10373	0.61	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig29926	AUGUSTUS	intron	10418	11617	0.61	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig29926	AUGUSTUS	intron	11743	11889	0.57	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig29926	AUGUSTUS	CDS	9226	9449	0.97	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig29926	AUGUSTUS	CDS	10374	10417	0.61	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig29926	AUGUSTUS	CDS	11618	11742	0.34	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [ggagcacagttattctgcccacatcatgttggtcactacctaggaatggaagtacttgatacaccgcttatctccaaag
# ataggaaattacagccgggcatgattctgaccatagaaccaggtttatttcacctgcgtaatccttttggcaagcctcttccacttgcatgtttgtat
# ttacgaccggaatttgtgccacataaattaagcttgttccgagggacagctataagactagctgaaaatatcttagtgactaaagatggacccatcaa
# tttatccgaaaatgtgtctccgcgtgaaaaagccacactggcctgtgacactgaatcctgttggtacagcgaggagcttcagaatttcatgggatctc
# tgctaatgcggatggtttag]
# protein sequence = [GAQLFCPHHVGHYLGMEVLDTPLISKDRKLQPGMILTIEPGLFHLRNPFGKPLPLACLYLRPEFVPHKLSLFRGTAIR
# LAENILVTKDGPINLSENVSPREKATLACDTESCWYSEELQNFMGSLLMRMV]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370HBN.prfl --predictionStart=0  --predictionEnd=23834  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2992620180911_busco_2432604931_.temp