# 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
# --[4..41]--> unknown_A (47) <--[1..134]--> unknown_B (74) <--[0..43]--> unknown_C (11) <--[4..11]--> unknown_D (80) <--[2..40]--> unknown_E (12) <--[0..1]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_4211cbai_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 = 7775, name = contig_4211) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
contig_4211	AUGUSTUS	gene	4405	9156	0.01	-	.	g1
contig_4211	AUGUSTUS	transcript	4405	9156	0.01	-	.	g1.t1
contig_4211	AUGUSTUS	tts	4405	4405	.	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_4211	AUGUSTUS	exon	4405	6131	.	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_4211	AUGUSTUS	stop_codon	5702	5704	.	-	0	transcript_id "g1.t1"; gene_id "g1";
contig_4211	AUGUSTUS	intron	6132	6413	0.61	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_4211	AUGUSTUS	CDS	5702	6131	0.62	-	1	transcript_id "g1.t1"; gene_id "g1";
contig_4211	AUGUSTUS	CDS	6414	6778	0.61	-	0	transcript_id "g1.t1"; gene_id "g1";
contig_4211	AUGUSTUS	exon	6414	7574	.	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_4211	AUGUSTUS	start_codon	6776	6778	.	-	0	transcript_id "g1.t1"; gene_id "g1";
contig_4211	AUGUSTUS	exon	8954	9156	.	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_4211	AUGUSTUS	tss	9156	9156	.	-	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcagcctttcatagactactacgaggtgcttaacgtgagccgccacgccactcccgacgaagtgaagagagcctacc
# gccggctcgccctccttcaccacccggacaaaaacccggacgacgtggtggagtcggcggagcggttcaaggtgatcaaggccgccgcggacacgctc
# tccgacccccggcaggcggcgcgctatgaccgggagtaccgccagtacctccagaagaggaagaggcaggagcgaggcggggagagggaccacaagag
# gaggagacaggatcgcgaggcagaaaggccggacaagagaacacgccaccaagacgaggaggatgaaggcgaggatagcaatgaagacgatgactcgg
# agtccgaggacgagtccgagctgtcgacgccgtctgaagagtccgaggaagaagtcaaccctttctgtcgtagcgacgaccctgacttcgagccccag
# tccgaggcgtcgagtgactcttccaccgacgaggagtccgagggtgacgcgtccctcgacgaggagtgcgaggaggagtctgggaacgagacttcctc
# cagcgacggctcttcttggtcctgggaccccgcctttggcggcgcgtctggcgatgaggcggaggaggcctcggccacgggctctgagccagagtggc
# ggacctccacggactccgaggcggaggaggaggaggaggacagcaggcggaacaagagacagaaacggaagcgtggacacggcgggaaagaggccggt
# ggtcccagcaagagaggcagatcggagtga]
# protein sequence = [MQPFIDYYEVLNVSRHATPDEVKRAYRRLALLHHPDKNPDDVVESAERFKVIKAAADTLSDPRQAARYDREYRQYLQK
# RKRQERGGERDHKRRRQDREAERPDKRTRHQDEEDEGEDSNEDDDSESEDESELSTPSEESEEEVNPFCRSDDPDFEPQSEASSDSSTDEESEGDASL
# DEECEEESGNETSSSDGSSWSWDPAFGGASGDEAEEASATGSEPEWRTSTDSEAEEEEEDSRRNKRQKRKRGHGGKEAGGPSKRGRSE]
# 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/EOG091G0MI7.prfl --predictionStart=1602  --predictionEnd=11757  --species=fly --progress=true ./tmp/contig_4211cbai_genome_v1.01.fasta_145855183_.temp