# 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..232]--> unknown_A (16) <--[5..12]--> unknown_B (15) <--[3..20]--> unknown_C (32) <--[4..23]--> unknown_D (38) <--[10..17]--> unknown_E (13) <--[0..9]--> unknown_F (19) <--[0..1]--> unknown_G (58) <--[1..14]--> unknown_H (44) <--[6..9]--> unknown_J (21) <--[6..15]--> unknown_K (13) <--[2..11]--> unknown_L (11) <--[2..6]--> unknown_M (22) <--[0..1]--> unknown_N (11) <--[2..138]--> unknown_O (20) <--[0..5]--> unknown_P (17) <--[3..9]--> unknown_Q (14) <--[0..1]--> unknown_R (15) <--[16..26]--> unknown_T (17) <--[1..13]--> unknown_U (21) <--[0..1]--> unknown_V (40) <--[0..61]--> unknown_W (30) <--[9..71]--> unknown_Y (47) <--[0..1]--> unknown_Z (9) <--[0..23]--> unknown_AA (21) <--[1..4]--> unknown_AB (44) <--[0..51]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_3896cbai_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 = 8628, name = contig_3896) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
contig_3896	AUGUSTUS	gene	1	8075	0.03	-	.	g1
contig_3896	AUGUSTUS	transcript	1	8075	0.03	-	.	g1.t1
contig_3896	AUGUSTUS	intron	1	2790	0.61	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	intron	3039	3808	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	intron	3919	7492	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	intron	7622	7677	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	CDS	2791	3038	0.74	-	1	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	exon	2791	3038	.	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	CDS	3809	3918	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	exon	3809	3918	.	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	CDS	7493	7621	1	-	0	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	exon	7493	7621	.	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	CDS	7678	7686	0.62	-	0	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	exon	7678	7741	.	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	start_codon	7684	7686	.	-	0	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	exon	7848	8075	.	-	.	transcript_id "g1.t1"; gene_id "g1";
contig_3896	AUGUSTUS	tss	8075	8075	.	-	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggaatatgcacagattgtcattgactggctggaaaacataacctttgacagcttcaagaatacatgctactatgatg
# cagtggagtactttggaggctcacatatttcttgggaaaatactttgaagactctgaagaatgagagcagtggcgttgtgcagcccctgagaggttct
# cggccctcgtcaagtccctggatccggattcctctttgcgggagggccgactcctgcatgacttggatcagagatgtgtggaaagcagtagcatggag
# gatagccagtgatgaacgtttgccagtcaaagagcgtgccatctatggggccttgtgcggccacctgcgggccatgctgctgggctgtgaacaatggg
# aggacaccttgtgggcctacacgcagcaccatggtggaccagtgggtggaggaacggctcagagcagcaaccactcacttgcgacagcctccatcctc
# tacctaaggaatatcctgaagaaaa]
# protein sequence = [MEYAQIVIDWLENITFDSFKNTCYYDAVEYFGGSHISWENTLKTLKNESSGVVQPLRGSRPSSSPWIRIPLCGRADSC
# MTWIRDVWKAVAWRIASDERLPVKERAIYGALCGHLRAMLLGCEQWEDTLWAYTQHHGGPVGGGTAQSSNHSLATASILYLRNILKK]
# 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/EOG091G02HY.prfl --predictionStart=0  --predictionEnd=8628  --species=fly --progress=true ./tmp/contig_3896cbai_genome_v1.01.fasta_145855183_.temp