# 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..1177]--> unknown_A (50) <--[0..1]--> unknown_B (35) <--[0..8]--> unknown_C (10) <--[8..15]--> unknown_D (76) <--[0..6]--> unknown_E (59) <--[2..49]--> unknown_F (17) <--[0..2]--> unknown_G (46) <--[8..54]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_3011cbai_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 = 7243, name = contig_3011) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
contig_3011	AUGUSTUS	gene	1473	4028	0.05	+	.	g1
contig_3011	AUGUSTUS	transcript	1473	4028	0.05	+	.	g1.t1
contig_3011	AUGUSTUS	exon	1473	2377	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3011	AUGUSTUS	start_codon	2013	2015	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_3011	AUGUSTUS	intron	2378	2659	0.88	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3011	AUGUSTUS	CDS	2013	2377	0.93	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_3011	AUGUSTUS	CDS	2660	3122	0.88	+	1	transcript_id "g1.t1"; gene_id "g1";
contig_3011	AUGUSTUS	exon	2660	4028	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3011	AUGUSTUS	stop_codon	3120	3122	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_3011	AUGUSTUS	tts	4028	4028	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcagcctttcatagactactacgaggtgcttaacgtgagccgccacgccactcccgacgaagtgaagagagcctacc
# gccggctcgccctccttcaccacccggacaaaaacccggacgacgtggtggagtcggcggagcggttcaaggtgatcaaggccgccgcggacacgctc
# tccgacccccggcaggcggcgcgctatgaccgggagtaccgccagtacctccagaagaggaagaggcaggagcgaggcggggagagggaccacaagag
# gaggagacaggatcgcgaggcagaaaggccggacaagagaacacgccaccaagacgaggaggatgaaggcgaggatagcaatgaagacgatgactcgg
# agtccgaggacgagtccgagctgtcgacgccgtctgaagagtccgaggaagaagtcaaccctttctgtcgtagcgacgaccctgacttcgagccccag
# tccgaggcgtcgagtgactcttccaccgacgaggagtccgaggcgacgagtgactcttccaccgacgaggagtccgagggtgacgcgtccctcgacga
# cgagtgcgaggaggagtctgggaacgagacttcctccagcgacggctcttcttggtcctgggaccccgcctttggcggcgcgtctggcgatgaggcgg
# aggaggcctcggccacgggctctgagccagagtggcggacctccacggactccgaggcggaggaggaggaggacagcaggcggaacaagagacagaaa
# cggaagcgtggacacggcgggaaagaggccggtggtcccagcaagagaggcagatcggagtga]
# protein sequence = [MQPFIDYYEVLNVSRHATPDEVKRAYRRLALLHHPDKNPDDVVESAERFKVIKAAADTLSDPRQAARYDREYRQYLQK
# RKRQERGGERDHKRRRQDREAERPDKRTRHQDEEDEGEDSNEDDDSESEDESELSTPSEESEEEVNPFCRSDDPDFEPQSEASSDSSTDEESEATSDS
# STDEESEGDASLDDECEEESGNETSSSDGSSWSWDPAFGGASGDEAEEASATGSEPEWRTSTDSEAEEEEDSRRNKRQKRKRGHGGKEAGGPSKRGRS
# E]
# 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/EOG091G0GWF.prfl --predictionStart=0  --predictionEnd=7243  --species=fly --progress=true ./tmp/contig_3011cbai_genome_v1.01.fasta_145855183_.temp