# 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..249]--> unknown_A (14) <--[0..8]--> unknown_B (21) <--[0..1]--> unknown_C (22) <--[0..15]--> unknown_D (15) <--[0..1]--> unknown_E (16) <--[1..48]--> unknown_F (28) <--[0..20]--> unknown_G (40) <--[30..46]--> unknown_K (19) <--[0..25]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2605520180911_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 = 20274, name = Contig26055) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig26055	AUGUSTUS	gene	13452	20274	0.19	-	.	g1
Contig26055	AUGUSTUS	transcript	13452	20274	0.19	-	.	g1.t1
Contig26055	AUGUSTUS	stop_codon	13452	13454	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig26055	AUGUSTUS	intron	13608	14428	0.57	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26055	AUGUSTUS	intron	14546	14657	0.81	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26055	AUGUSTUS	intron	14708	15004	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26055	AUGUSTUS	intron	15177	19163	0.5	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26055	AUGUSTUS	intron	19312	20274	0.84	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26055	AUGUSTUS	CDS	13452	13607	0.91	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig26055	AUGUSTUS	CDS	14429	14545	0.57	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig26055	AUGUSTUS	CDS	14658	14707	0.98	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig26055	AUGUSTUS	CDS	15005	15176	0.94	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig26055	AUGUSTUS	CDS	19164	19311	0.62	-	1	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [ggttaaaaatgtggaggatgaactcctgaaggccagaaacgactgcaagaggttccaggcgaacttcgagggactcatt
# catgaaatggttgcagaagtggacgcactgatggatattgccgcttcctgttctaaagaaaagcaaaaggccaaaatgaagtggttacgaggggaaat
# tagagaccggataaaactggagcaagccttaaaaaaggatttacaggaggctttgtcatgcaatgaaacagatcgtcacttcctcatatcggagattg
# ccaagcgtgatggtgtaatggacgaactctcagtagtcaagcacgaacttagtcacagggaagctgaaaacttccactgtgttgagaaattgcagacc
# cagattttagatttaacggatgaacttgaactccgtaaaatccgtgaagatgagttgctgaggcagcaagccttggataataaacatgtgatcgaaga
# aattgaagaacttagagacgtacaggaggagaaggccagaattgaacaacgatacgtcaaattacaggacaccatgagggcattacagagcgaactca
# aatccacaaatttctacggtgacaaggtaccccattatgacatctcaagacccatcaatgatctaacattttag]
# protein sequence = [VKNVEDELLKARNDCKRFQANFEGLIHEMVAEVDALMDIAASCSKEKQKAKMKWLRGEIRDRIKLEQALKKDLQEALS
# CNETDRHFLISEIAKRDGVMDELSVVKHELSHREAENFHCVEKLQTQILDLTDELELRKIREDELLRQQALDNKHVIEEIEELRDVQEEKARIEQRYV
# KLQDTMRALQSELKSTNFYGDKVPHYDISRPINDLTF]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370UG9.prfl --predictionStart=0  --predictionEnd=20274  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2605520180911_busco_2432604931_.temp