# 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..13]--> unknown_A (105) <--[2..19]--> unknown_B (32) <--[0..16]--> unknown_C (54) <--[3..8]--> unknown_D (8) <--[0..17]--> unknown_E (21) <--[6..14]--> unknown_F (12) <--[19..46]--> unknown_G (39) <--[1..8]--> unknown_H (16) <--[0..12]--> unknown_I (6) <--[2..3]--> unknown_J (29) <--[11..20]--> unknown_L (9) <--[19..55]--> unknown_M (10) <--[3..23]--> unknown_N (18) <--[13..40]--> unknown_P (54) <--[0..15]--> unknown_Q (27) <--[0..48]--> unknown_R (20) <--[17..69]--> unknown_T (42) <--[0..1]--> unknown_U (59) <--[0..202]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4845120180911_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 = 12110, name = Contig48451) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig48451	AUGUSTUS	gene	1	8727	0.07	-	.	g1
Contig48451	AUGUSTUS	transcript	1	8727	0.07	-	.	g1.t1
Contig48451	AUGUSTUS	intron	1	1680	0.28	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	intron	1806	4747	0.7	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	intron	4845	6261	0.82	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	intron	6384	7627	0.69	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	intron	7744	8047	0.46	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	intron	8070	8545	0.42	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	CDS	1681	1805	0.26	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	CDS	4748	4844	0.87	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	CDS	6262	6383	0.82	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	CDS	7628	7743	0.74	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	CDS	8048	8069	0.46	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	CDS	8546	8727	0.86	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig48451	AUGUSTUS	start_codon	8725	8727	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcttataaatcctacaggtttgaatggctggacccaagcatcaagaagacagagtggagtcgagaagaagaagaaa
# agttgctgcatttggccaagctgatgccaactcaatggagaaccatagcgccgatcgtgggacgaactgcagcacaatgcctggaacactatgaatat
# ctgcttaactctctgattgtctgtacttgttcactgaactctctgattgtgttcgtgatgttccataactctctgattggtcactgtgacttcagaac
# tcttctgattgtgtacttgagtgttcagaaactcctatttgtactagacaaagctcaaaaccgagatgacagtgaaggtgatcccaggaaacttaaac
# caggagaaattgatcccaatccagagaccaagccagccaaaccagaccctattgatatggatgaagatgagctggagatgttgtctgaagcgagagca
# cgattagccaacacacagggtaaaaaggcaaagagaaaagccagggaaaaacagctggaagaagcaagagatagaggacaaaaggaacgagagaaaga
# cgaggagtggagtggcgtaaaaaaaaagagaagtggattgacaatgcttgaaggaatcccatgtttcgagaaaagaagaaacctgcacagggtat]
# protein sequence = [MAYKSYRFEWLDPSIKKTEWSREEEEKLLHLAKLMPTQWRTIAPIVGRTAAQCLEHYEYLLNSLIVCTCSLNSLIVFV
# MFHNSLIGHCDFRTLLIVYLSVQKLLFVLDKAQNRDDSEGDPRKLKPGEIDPNPETKPAKPDPIDMDEDELEMLSEARARLANTQGKKAKRKAREKQL
# EEARDRGQKEREKDEEWSGVKKKRSGLTMLEGIPCFEKRRNLHRV]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093702AT.prfl --predictionStart=0  --predictionEnd=28748  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4845120180911_busco_2432604931_.temp