# 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..222]--> unknown_A (15) <--[0..3]--> unknown_B (23) <--[0..18]--> unknown_C (35) <--[0..18]--> unknown_D (63) <--[0..143]--> unknown_E (8) <--[0..1]--> unknown_F (15) <--[6..9]--> unknown_H (17) <--[0..3]--> unknown_I (19) <--[0..2]--> unknown_J (70) <--[4..12]--> unknown_K (13) <--[0..1]--> unknown_L (93) <--[0..2]--> unknown_M (17) <--[1..2]--> unknown_N (26) <--[4..11]--> unknown_O (81) <--[0..8]--> unknown_P (8) <--[3..11]--> unknown_Q (48) <--[2..148]--> unknown_R (26) <--[10..42]--> unknown_S (17) <--[3..30]--> unknown_T (10) <--[0..18]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig10301020180911_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 = 2130, name = Contig103010) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig103010	AUGUSTUS	gene	1	1874	0.39	+	.	g1
Contig103010	AUGUSTUS	transcript	1	1874	0.39	+	.	g1.t1
Contig103010	AUGUSTUS	intron	1	147	0.52	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig103010	AUGUSTUS	intron	343	885	0.94	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig103010	AUGUSTUS	intron	1023	1134	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig103010	AUGUSTUS	intron	1223	1448	0.99	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig103010	AUGUSTUS	intron	1591	1692	0.73	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig103010	AUGUSTUS	CDS	148	342	0.53	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig103010	AUGUSTUS	CDS	886	1022	0.95	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig103010	AUGUSTUS	CDS	1135	1222	0.99	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig103010	AUGUSTUS	CDS	1449	1590	0.75	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig103010	AUGUSTUS	CDS	1693	1874	0.98	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig103010	AUGUSTUS	stop_codon	1872	1874	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [actataccagcccgcatgtttaggcgggttctgactatcgtgaacgcccactgcaagcttggactgaccgcaacattgg
# tacgggaggatgacaaaattgcggacctgaactttctgattggaccaaagctgtatgaagcgaactggatggagctacagaataacgggtacatcgcc
# agagtgcagtgtgcagagttgttggcagttgtgaatcctaacaagtttcgagcttgccagttcctgatccgataccatgaaagacgcaacgacaaaat
# cattgtgttctcggataatgtgtttgccctgaaaagttacgccattaaactgaacaagccatacttgtatggacccacctcacaaggggagagaatgc
# agatcttgcagaactttgtccataatccaaaagtcaacaccatctttgtggccgacacttcctttgacctcccagaagccaacgtgctaattcagatc
# tcggcccacgggggctcgcgtcgacaggaggcccagaggatgggcagaattctcagggccaaaaagggtaatcatagtgtacatgttagcagagctgt
# agcggaggaatacaatgcgttcttttattccctggtttcccaggataccatggagatgcacttctctctgaagaggcagaggctttcgtcaacgaggg
# ctatgcttactagatttggtctcaccaaatctcgccggcaatggaaggaccaggttaaggggcaacttctcaactga]
# protein sequence = [TIPARMFRRVLTIVNAHCKLGLTATLVREDDKIADLNFLIGPKLYEANWMELQNNGYIARVQCAELLAVVNPNKFRAC
# QFLIRYHERRNDKIIVFSDNVFALKSYAIKLNKPYLYGPTSQGERMQILQNFVHNPKVNTIFVADTSFDLPEANVLIQISAHGGSRRQEAQRMGRILR
# AKKGNHSVHVSRAVAEEYNAFFYSLVSQDTMEMHFSLKRQRLSSTRAMLTRFGLTKSRRQWKDQVKGQLLN]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093703C8.prfl --predictionStart=0  --predictionEnd=21766  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig10301020180911_busco_2432604931_.temp