# 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/Contig2992820180911_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 = 7798, name = Contig29928) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig29928	AUGUSTUS	gene	1	4630	0.18	+	.	g1
Contig29928	AUGUSTUS	transcript	1	4630	0.18	+	.	g1.t1
Contig29928	AUGUSTUS	intron	1	1019	0.32	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	intron	1053	2212	0.53	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	intron	2346	3308	0.57	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	intron	3365	3501	0.83	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	intron	3588	3813	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	intron	4040	4507	0.96	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	CDS	1020	1052	0.31	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	CDS	2213	2345	0.56	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	CDS	3309	3364	0.72	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	CDS	3502	3587	0.86	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	CDS	3814	4039	0.99	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	CDS	4508	4630	0.71	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig29928	AUGUSTUS	stop_codon	4628	4630	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ctgcagcatgccttgtatgtcagggaagccgcagctaaaggtgtacctgtggtgcgtcgtcctgacagaaaagatttgt
# tgtcctatctaaatggagaaacctcgtcatctgcaaacatcgacaagagcgctcctctggaaattccattacaaaaaattccacaagccaaaagagga
# gcaatagacactcatgaaggagataaaaagaaaccaaggctagaggagaaacaagtacaagaggcccgattaaactggatcaacaaaatcgacgcccc
# gagagagacttctgtccttcctgctgctttagcttcctcgtccttgccagaagcaatgcccttagaaaagattgctgccatcaaagccaaaagattgg
# caaaaaagcgaacaatgattaaagtggatgaaaatgacattcagtcgggtgccctggaacagagaagcttcgtcgatgctgaagtggacgttaccaga
# gatattgtcagcagagaaagattatggcgaacgagaacaacaattctacagagtcaaggaaaacaatttgcaaagaacatctttggaattctgcaatc
# aataaaagccagagaggaaggcacacagaaacaccaccctgctcctcatactccatctgtggtgagtcataggtgtgcagcctggtga]
# protein sequence = [LQHALYVREAAAKGVPVVRRPDRKDLLSYLNGETSSSANIDKSAPLEIPLQKIPQAKRGAIDTHEGDKKKPRLEEKQV
# QEARLNWINKIDAPRETSVLPAALASSSLPEAMPLEKIAAIKAKRLAKKRTMIKVDENDIQSGALEQRSFVDAEVDVTRDIVSRERLWRTRTTILQSQ
# GKQFAKNIFGILQSIKAREEGTQKHHPAPHTPSVVSHRCAAW]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370HBN.prfl --predictionStart=0  --predictionEnd=22398  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2992820180911_busco_2432604931_.temp