# 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/scaffold_3119cbai_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 = 10328, name = scaffold_3119) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
scaffold_3119	AUGUSTUS	gene	6988	16601	0.01	+	.	g1
scaffold_3119	AUGUSTUS	transcript	6988	16601	0.01	+	.	g1.t1
scaffold_3119	AUGUSTUS	tss	6988	6988	.	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	exon	6988	7455	.	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	exon	10153	11030	.	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	exon	11146	11613	.	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	start_codon	11241	11243	.	+	0	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	intron	11614	11776	0.39	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	intron	12064	12136	0.86	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	intron	12443	12513	0.72	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	intron	12676	13815	0.51	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	CDS	11241	11613	0.17	+	0	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	CDS	11777	12063	0.43	+	2	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	exon	11777	12063	.	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	CDS	12137	12442	0.88	+	0	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	exon	12137	12442	.	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	CDS	12514	12675	0.49	+	0	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	exon	12514	12675	.	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	CDS	13816	15933	0.46	+	0	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	exon	13816	16601	.	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	stop_codon	15931	15933	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggagcagaggagtataacaatgaaagtcaagaccctgacgccaccagccatgccaggacccagcgccaccaagaccc
# ccaagcagggcaccaaggcgggctgctgtgccttcctgcgtgccttcctcaggatgtttaaaaggaagaagcacgcacgtcactcctccagcgggcgc
# ctgacagagcctgcgatggaggagcctgttgtggaggagtgcccggggcctgaccatcagtctgccccgctggaccaagcaccggaagagctggtgaa
# gaagggggaaacagagtgtgtcgaggagcaggtgcagatggagggtggaggagcacgaggaagtattggatgtgcagaagacggcggagacagagaag
# actccgaggagtcgtcttcagaggagtcttccaagcctgcaccgcctgtcaagaaccagcgaggcaaggcacagaacaacagagccaagaaggacgct
# gccccgccctccgccgcgcccgagctgctgctgcggccacgcggcgctgtgatcaccttccgcagcgacgtggtggacccgcccgccaccctcctcat
# gggctccgacaagcacgagaacgaccacctcctggcgcaggccacggaccgcctcgtgttcttccacgtggacgccctgccctcggcccacctgtgca
# aggccaacagtgccaagggcaacaggctgggcaacgtggtggtggtgtacacgctgggatcgaacctgagcaagacccgccacatgaaggccggcgag
# gtgggcttcgtctgcgaccgggaggtgcgcaagatcctcgtctccaagcgggacgacaagatcatggaccgcctcaacaccaccaagaggaaggtcct
# ctcacgcaggtcggagcgggagaagcagcagcgggccaaggagaggcagcgccagaagactgaggcaaagttgaagaacagaaagcagaagcaggagc
# agcaacagcctcccgccgcctgcaccgctggcaagccgcgacgcaggcgacgggagcgccgtgagttggacagctcagatgaagagtgtggtgatgaa
# aagcagcagaaggagacaacggagaaggagaccaccctgccggagacagtgacgacacgctgcttcccgtgttcctgcctcaacacacatcacctctc
# atcatcacttctaccttaccatcacttctctgccagtgttcctgcctcaacactcatcacctctcatcatcacttctctctgccagtgttcctgcctc
# aacacacatcacttctctaccatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctg
# ccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacacacatcacctctc
# atcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgc
# cagtgttcctgcctcaacactcatcacttctcatcatcacttctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctacctta
# ccatcactcctctgccagtgttcctgcctcaacactcatcacctcctctcaccttaccatcactcctctgccagtgttcctgcctcaacactcatcac
# ttctaccttaccatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttc
# ctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacactcatcacttctcatcatcact
# tctaccttaccatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcc
# tgcctcaacacacatcacctctcatcatcacttctaccttaccatcacttctctgccagtgttcctgcctcaacacacatcacctctcatcaccactt
# ctaccttaccatcacttctctgccagtgttcctgcctcaacactcatcacctctcatcatcacttctaccttaccatcacttctctgccagtgttcct
# gcctcaacacacatcacctctcatcaccacttctaccttaccatcacttctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttc
# taccttaccatcacttctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcacttctctgccagtgttcctg
# cctcaacacacatcacctctcatcatcacttctaccttaccatcacttctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttct
# accttaccatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcacttctctgccagtgttcctgc
# ctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcttctgcctcgccacacatcacctctcatcatcacttc
# taccttaccatcacttctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcctg
# cctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcaccacttct
# accttaccatcactcctctgccagtgttcctgcctcaacactcatcacctctcatcatcacttctaccttaccatcactctctgccagtgttcctgcc
# tcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctac
# cttaccatcacttctctgccagtgttcctgcctcaacacacatcacctctcatcaccacttcaccttaccatcacttctctgccagtacctgctcact
# accttacctgaccagaccagacctgttctaa]
# protein sequence = [MEQRSITMKVKTLTPPAMPGPSATKTPKQGTKAGCCAFLRAFLRMFKRKKHARHSSSGRLTEPAMEEPVVEECPGPDH
# QSAPLDQAPEELVKKGETECVEEQVQMEGGGARGSIGCAEDGGDREDSEESSSEESSKPAPPVKNQRGKAQNNRAKKDAAPPSAAPELLLRPRGAVIT
# FRSDVVDPPATLLMGSDKHENDHLLAQATDRLVFFHVDALPSAHLCKANSAKGNRLGNVVVVYTLGSNLSKTRHMKAGEVGFVCDREVRKILVSKRDD
# KIMDRLNTTKRKVLSRRSEREKQQRAKERQRQKTEAKLKNRKQKQEQQQPPAACTAGKPRRRRRERRELDSSDEECGDEKQQKETTEKETTLPETVTT
# RCFPCSCLNTHHLSSSLLPYHHFSASVPASTLITSHHHFSLPVFLPQHTSLLYHHSSASVPASTHITSHHHFYLTITPLPVFLPQHTSPLIITSTLPS
# LLCQCSCLNTHHLSSSLLPYHHSSASVPASTHITSHHHFYLTITPLPVFLPQHSSLLIITSLPVFLPQHTSPLIITSTLPSLLCQCSCLNTHHLLSPY
# HHSSASVPASTLITSTLPSLLCQCSCLNTHHLSSSLLPYHHSSASVPASTHITSHHHFYLTITPLPVFLPQHSSLLIITSTLPSLLCQCSCLNTHHLS
# SSLLPYHHSSASVPASTHITSHHHFYLTITSLPVFLPQHTSPLITTSTLPSLLCQCSCLNTHHLSSSLLPYHHFSASVPASTHITSHHHFYLTITSLP
# VFLPQHTSPLIITSTLPSLLCQCSCLNTHHLSSSLLPYHHFSASVPASTHITSHHHFYLTITSLPVFLPQHTSPLIITSTLPSLLCQCSCLNTHHLSS
# SLLPYHHFSASVPASTHITSHHHFYLTITPLPVFFCLATHHLSSSLLPYHHFSASVPASTHITSHHHFYLTITPLPVFLPQHTSPLIITSTLPSLLCQ
# CSCLNTHHLSSPLLPYHHSSASVPASTLITSHHHFYLTITLCQCSCLNTHHLSSSLLPYHHSSASVPASTHITSHHHFYLTITSLPVFLPQHTSPLIT
# TSPYHHFSASTCSLPYLTRPDLF]
# 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=6923  --predictionEnd=17250  --species=fly --progress=true ./tmp/scaffold_3119cbai_genome_v1.01.fasta_145855183_.temp