# 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 (41) <--[1..6]--> unknown_B (42) <--[0..3]--> unknown_C (16) <--[0..2]--> unknown_D (78) <--[0..1]--> unknown_E (27) <--[5..57]--> unknown_F (13) <--[0..15]--> unknown_G (15) <--[1..43]--> unknown_H (13) <--[1..7]--> unknown_I (13) <--[0..34]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig7273620180911_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 = 10961, name = Contig72736) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig72736	AUGUSTUS	gene	5928	8741	0.28	+	.	g1
Contig72736	AUGUSTUS	transcript	5928	8741	0.28	+	.	g1.t1
Contig72736	AUGUSTUS	start_codon	5928	5930	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig72736	AUGUSTUS	intron	6104	8087	0.52	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig72736	AUGUSTUS	intron	8096	8652	0.47	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig72736	AUGUSTUS	CDS	5928	6103	0.57	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig72736	AUGUSTUS	CDS	8088	8095	0.5	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig72736	AUGUSTUS	CDS	8653	8741	0.49	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig72736	AUGUSTUS	stop_codon	8739	8741	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtgtgtaccaagtttggtgaatttggcccagcggttcttgagaagaagtcgaaaatgtcaaaagtctaacagacaga
# cggaacggacggaacggcagacaggacagacagacggacagacagacagcgacgcagcaaaaggcgatcagaaaagctcacttgagccttcggtcagt
# gctccaggtaggtggaagagaaaaattaagaagttctttatggaagatacagaatggaagagtggaagaaaaagagaaactcataatgaaaaatag]
# protein sequence = [MCVPSLVNLAQRFLRRSRKCQKSNRQTERTERQTGQTDGQTDSDAAKGDQKSSLEPSVSAPGRWKRKIKKFFMEDTEW
# KSGRKRETHNEK]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370L23.prfl --predictionStart=0  --predictionEnd=29172  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig7273620180911_busco_2432604931_.temp