# 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
# --[11..184]--> unknown_B (41) <--[0..3]--> unknown_C (64) <--[0..1]--> unknown_D (15) <--[0..1]--> unknown_E (11) <--[3..38]--> unknown_F (45) <--[0..13]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_3442cbai_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 = 9095, name = contig_3442) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
contig_3442	AUGUSTUS	gene	646	4910	0.01	+	.	g1
contig_3442	AUGUSTUS	transcript	646	4910	0.01	+	.	g1.t1
contig_3442	AUGUSTUS	tss	646	646	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	exon	646	743	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	exon	2187	2878	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	exon	2991	3788	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	start_codon	3084	3086	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	intron	3789	3858	0.97	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	intron	4287	4356	0.62	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	intron	4515	4589	0.72	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	CDS	3084	3788	0.76	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	CDS	3859	4286	0.69	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	exon	3859	4286	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	CDS	4357	4514	0.62	+	1	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	exon	4357	4514	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	CDS	4590	4795	0.72	+	2	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	exon	4590	4910	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	stop_codon	4793	4795	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_3442	AUGUSTUS	tts	4910	4910	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggagcagaagagtataacaatgaaactcaagaccttcacgccaccagccatgccaggacccagcgccaccaagaccc
# ccaaggagggcaccaaggcgggctgctgtgccttcgtgcgcgccttcctcaggatgttcaaaaggaagaagcgcgcacgtcactcctccagcgggcgc
# ctgacggagcctgcgatcgaggaccctgttgtggaggagtccccggggcctgaccagcagtctgccccgctggaccaagcaccggaagagctggtgaa
# gaagagggaagaagaatgtgtcgaggaggagcaggtggagcaagaagagcaggtggaggagcacacagaagtattggatgcacagaagacggttgaga
# cggagaaggttgtggaggagacggagacggagatgggtgtgataaggcgtgttgaggaggagcaggaagtgaaggaggtgaaggaggaggagcagact
# gtgcaggaacctgttgtggcagagcaggttccggaagactcatcactgaaggttcatgacgccgacgattccgactctgaggagtcgtcttcagagga
# gtcttccaagcctgcaccgcctgtcaagaaccagcgaggcaaggcccagaacaacagagccaagaaggacgctgcctctgccgcgcccgagctgctgc
# tgcggccacgcggcgctgtgatcaccttccgcagcgacgccacggaccgcctcgtgttcttccatgtggacgacttgccctcggcccacgtgtacctc
# cagctggagcccggccaggccctgcgcgacgtgccccgcgtccttctgaacgacgcggcacagctgtgcaaggccaacagtgccaagggcaacaggct
# gggcaacgtggtggtggtgtacacgctgggatcgaacctgagcaagacccgccacatgaaggccggcgaggtgggcttcgtctgcgacaaggaggtgc
# gcaagatccttgtctcccggcgggacgacagggtcatggaccgcctcaacaacaccaagaggaaggtcctctcacgcaagtcggagcgggagaagcag
# cagcgggccaaggagaggcagcggcagaagaccgaggctaagttgaagaaaagaaagcagaagcaggagcagcacagcgtcccgccgcctgcaccgct
# ggcaagccgcgacgcaggcgacgggagcggcgcgaggaggatagctcagacgaagagtctggtgatgaaagagagagcgagaaacggagaaggagaca
# accctgccggagaaggagacgacacgcggcttcccgccccacgcaagggtgaggccgagggccgcggcaccgtcacgggggctcccgacgacgtggct
# tacgccctggctgagctcaagaagctgctgtttcctgagcagcagaaggcagcggccgcgcctcaggacaacaagggcggcaagggcagagaggccaa
# gggtcccagcaccaagggctcctccaaacagaagagaaaggagtga]
# protein sequence = [MEQKSITMKLKTFTPPAMPGPSATKTPKEGTKAGCCAFVRAFLRMFKRKKRARHSSSGRLTEPAIEDPVVEESPGPDQ
# QSAPLDQAPEELVKKREEECVEEEQVEQEEQVEEHTEVLDAQKTVETEKVVEETETEMGVIRRVEEEQEVKEVKEEEQTVQEPVVAEQVPEDSSLKVH
# DADDSDSEESSSEESSKPAPPVKNQRGKAQNNRAKKDAASAAPELLLRPRGAVITFRSDATDRLVFFHVDDLPSAHVYLQLEPGQALRDVPRVLLNDA
# AQLCKANSAKGNRLGNVVVVYTLGSNLSKTRHMKAGEVGFVCDKEVRKILVSRRDDRVMDRLNNTKRKVLSRKSEREKQQRAKERQRQKTEAKLKKRK
# QKQEQHSVPPPAPLASRDAGDGSGARRIAQTKSLVMKERARNGEGDNPAGEGDDTRLPAPRKGEAEGRGTVTGAPDDVAYALAELKKLLFPEQQKAAA
# APQDNKGGKGREAKGPSTKGSSKQKRKE]
# 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/EOG091G0LS0.prfl --predictionStart=0  --predictionEnd=9095  --species=fly --progress=true ./tmp/contig_3442cbai_genome_v1.01.fasta_145855183_.temp