# 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
# --[7..82]--> unknown_B (14) <--[0..5]--> unknown_C (19) <--[3..9]--> unknown_D (17) <--[10..34]--> unknown_E (25) <--[0..11]--> unknown_F (18) <--[3..23]--> unknown_G (33) <--[39..317]--> unknown_H (49) <--[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/Contig4533620180911_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 = 2711, name = Contig45336) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig45336	AUGUSTUS	gene	1	2711	0.76	-	.	g1
Contig45336	AUGUSTUS	transcript	1	2711	0.76	-	.	g1.t1
Contig45336	AUGUSTUS	intron	1	490	0.94	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45336	AUGUSTUS	intron	600	1540	0.87	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45336	AUGUSTUS	intron	1617	2320	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45336	AUGUSTUS	intron	2590	2711	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig45336	AUGUSTUS	CDS	491	599	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig45336	AUGUSTUS	CDS	1541	1616	0.89	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig45336	AUGUSTUS	CDS	2321	2589	0.95	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [caaaaacaagcttgtccagaagattcaccaatcagaaatgaggtcataggtcaagcccatgtggagaactatgccctga
# aagtgtttctctatgcagacaatgaagacagagctggcagatttaacaagtacgaagatctactgtttttgttcacagatacaagtttcacaatgtca
# gcttctttcatcaggccaaaacaaaataaagatgtgtttcagattacccgaacaaccctaaaattttctcccgacccccaaccctttgagatgaatgt
# ggtgaaatctttttacacggctgggatgctgtttgacgttctgtccgtctttgatctcgtcagtgaagatatagaaaagaacaaaaaatacgccaaat
# ggaaggcagcgtatattcacaaatgtctgcggaatggcgagacccccgtagcggggcccctaccagaggaggacgacgaag]
# protein sequence = [QKQACPEDSPIRNEVIGQAHVENYALKVFLYADNEDRAGRFNKYEDLLFLFTDTSFTMSASFIRPKQNKDVFQITRTT
# LKFSPDPQPFEMNVVKSFYTAGMLFDVLSVFDLVSEDIEKNKKYAKWKAAYIHKCLRNGETPVAGPLPEEDDE]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370GC2.prfl --predictionStart=0  --predictionEnd=22550  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4533620180911_busco_2432604931_.temp