# 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..16]--> unknown_A (21) <--[7..13]--> unknown_B (30) <--[0..4]--> unknown_C (15) <--[10..32]--> unknown_D (16) <--[1..50]--> unknown_E (12) <--[6..34]--> unknown_G (43) <--[0..17]--> unknown_H (23) <--[0..5]--> unknown_I (34) <--[0..3]--> unknown_J (17) <--[5..25]--> unknown_K (15) <--[0..3]--> unknown_L (13) <--[0..16]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig16965520180911_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 = 6923, name = Contig169655) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig169655	AUGUSTUS	gene	1	1162	0.09	-	.	g1
Contig169655	AUGUSTUS	transcript	1	1162	0.09	-	.	g1.t1
Contig169655	AUGUSTUS	intron	1	274	0.66	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig169655	AUGUSTUS	intron	431	525	0.68	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig169655	AUGUSTUS	intron	632	1157	0.13	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig169655	AUGUSTUS	CDS	275	430	0.73	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig169655	AUGUSTUS	CDS	526	631	0.36	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig169655	AUGUSTUS	CDS	1158	1162	0.21	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig169655	AUGUSTUS	start_codon	1160	1162	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggggaaggactcaggagaatgcagnnnnnnnnnnnnnnnnnnnnnnnnngagattgatgaagacagcatacttacac
# aactggctcaggcctggtttaatctcactgtgggaggggagaagtaccaggatgcatactacatttttcaagagatggcagacaaacacaattctacg
# cccctcctactgaatggtcaggctgcctgttacatcgcacagggaaaatttgatgatgcagaatctgtgttacaggaagccatggataag]
# protein sequence = [MGKDSGECXXXXXXXXXEIDEDSILTQLAQAWFNLTVGGEKYQDAYYIFQEMADKHNSTPLLLNGQAACYIAQGKFDD
# AESVLQEAMDK]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370OGW.prfl --predictionStart=0  --predictionEnd=20585  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig16965520180911_busco_2432604931_.temp