# 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 /gscratch/scrubbed/samwhite/outputs/20200924_cbai_genome_v1.01_busco/cbai_genome_v1.01.fasta_augustus/config/ ...
# Using protein profile unknown
# --[0..46]--> unknown_A (27) <--[2..3]--> unknown_B (28) <--[1..5]--> unknown_C (87) <--[0..1]--> unknown_D (41) <--[6..9]--> unknown_E (13) <--[0..51]--> unknown_F (61) <--[0..4]--> unknown_G (48) <--[0..294]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_1441cbai_genome_v1.01.fasta_145855183_.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 = 9440, name = contig_1441) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
contig_1441	AUGUSTUS	gene	8654	18039	0.02	+	.	g1
contig_1441	AUGUSTUS	transcript	8654	18039	0.02	+	.	g1.t1
contig_1441	AUGUSTUS	exon	8654	9172	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_1441	AUGUSTUS	start_codon	9143	9145	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_1441	AUGUSTUS	intron	9173	9998	0.96	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_1441	AUGUSTUS	intron	10080	12927	0.06	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_1441	AUGUSTUS	intron	13063	18039	0.02	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_1441	AUGUSTUS	CDS	9143	9172	0.96	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_1441	AUGUSTUS	CDS	9999	10079	0.96	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_1441	AUGUSTUS	exon	9999	10079	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_1441	AUGUSTUS	CDS	12928	13062	0.05	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_1441	AUGUSTUS	exon	12928	13062	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggaagatgttttctcctcaggagttgaggttggagatgactataccaaaattaatcccatgggccagattccagcgc
# tggtcgtcggtgacaagacgttgacccagtcggttcaaggtggatttgtcccagttccccatcatcaaccgaatccacgaggccctcggcaccttgga
# gccctctcaaggctgccctcccgccaaccagcccgactgcccggaggacctcaaatagtgctgcacaag]
# protein sequence = [MEDVFSSGVEVGDDYTKINPMGQIPALVVGDKTLTQSVQGGFVPVPHHQPNPRGPRHLGALSRLPSRQPARLPGGPQI
# VLHK]
# end gene g1
###
# command line:
# /gscratch/srlab/programs/Augustus-3.3.2/bin/augustus --codingseq=1 --proteinprofile=/gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/prfl/EOG091G0E5O.prfl --predictionStart=8600  --predictionEnd=18770  --species=fly --progress=true ./tmp/contig_1441cbai_genome_v1.01.fasta_145855183_.temp