# 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
# --[2..99]--> unknown_A (24) <--[0..2]--> unknown_B (119) <--[0..13]--> unknown_C (22) <--[6..16]--> unknown_E (10) <--[0..30]--> unknown_F (20) <--[4..44]--> unknown_G (41) <--[0..22]--> unknown_H (39) <--[2..8]--> unknown_I (11) <--[0..5]--> unknown_J (37) <--[0..15]--> unknown_K (30) <--[3..12]--> unknown_L (29) <--[3..58]--> unknown_M (92) <--[12..53]--> unknown_N (10) <--[0..2]--> unknown_O (14) <--[0..9]--> unknown_P (19) <--[7..14]--> unknown_Q (10) <--[0..83]--
# 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 = 16214, name = scaffold_3119) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
scaffold_3119	AUGUSTUS	gene	13405	16354	0.08	+	.	g1
scaffold_3119	AUGUSTUS	transcript	13405	16354	0.08	+	.	g1.t1
scaffold_3119	AUGUSTUS	intron	13405	13880	0.56	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	CDS	13881	15933	0.44	+	1	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	exon	13881	16354	.	+	.	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	stop_codon	15931	15933	.	+	0	transcript_id "g1.t1"; gene_id "g1";
scaffold_3119	AUGUSTUS	tts	16354	16354	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [tgttcctgcctcaacactcatcacctctcatcatcacttctctctgccagtgttcctgcctcaacacacatcacttctc
# taccatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctca
# acacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctacctt
# accatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaa
# cactcatcacttctcatcatcacttctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgcca
# gtgttcctgcctcaacactcatcacctcctctcaccttaccatcactcctctgccagtgttcctgcctcaacactcatcacttctaccttaccatcac
# tcctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacacacatc
# acctctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacactcatcacttctcatcatcacttctaccttaccatcact
# cctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacacacatca
# cctctcatcatcacttctaccttaccatcacttctctgccagtgttcctgcctcaacacacatcacctctcatcaccacttctaccttaccatcactt
# ctctgccagtgttcctgcctcaacactcatcacctctcatcatcacttctaccttaccatcacttctctgccagtgttcctgcctcaacacacatcac
# ctctcatcaccacttctaccttaccatcacttctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcacttc
# tctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcacttctctgccagtgttcctgcctcaacacacatcacc
# tctcatcatcacttctaccttaccatcacttctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcct
# ctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcacttctctgccagtgttcctgcctcaacacacatcacct
# ctcatcatcacttctaccttaccatcactcctctgccagtgttcttctgcctcgccacacatcacctctcatcatcacttctaccttaccatcacttc
# tctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacacacatcacc
# tctcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcaccacttctaccttaccatcactcct
# ctgccagtgttcctgcctcaacactcatcacctctcatcatcacttctaccttaccatcactctctgccagtgttcctgcctcaacacacatcacctc
# tcatcatcacttctaccttaccatcactcctctgccagtgttcctgcctcaacacacatcacctctcatcatcacttctaccttaccatcacttctct
# gccagtgttcctgcctcaacacacatcacctctcatcaccacttcaccttaccatcacttctctgccagtacctgctcactaccttacctgaccagac
# cagacctgttctaa]
# protein sequence = [VPASTLITSHHHFSLPVFLPQHTSLLYHHSSASVPASTHITSHHHFYLTITPLPVFLPQHTSPLIITSTLPSLLCQCS
# CLNTHHLSSSLLPYHHSSASVPASTHITSHHHFYLTITPLPVFLPQHSSLLIITSLPVFLPQHTSPLIITSTLPSLLCQCSCLNTHHLLSPYHHSSAS
# VPASTLITSTLPSLLCQCSCLNTHHLSSSLLPYHHSSASVPASTHITSHHHFYLTITPLPVFLPQHSSLLIITSTLPSLLCQCSCLNTHHLSSSLLPY
# HHSSASVPASTHITSHHHFYLTITSLPVFLPQHTSPLITTSTLPSLLCQCSCLNTHHLSSSLLPYHHFSASVPASTHITSHHHFYLTITSLPVFLPQH
# TSPLIITSTLPSLLCQCSCLNTHHLSSSLLPYHHFSASVPASTHITSHHHFYLTITSLPVFLPQHTSPLIITSTLPSLLCQCSCLNTHHLSSSLLPYH
# HFSASVPASTHITSHHHFYLTITPLPVFFCLATHHLSSSLLPYHHFSASVPASTHITSHHHFYLTITPLPVFLPQHTSPLIITSTLPSLLCQCSCLNT
# HHLSSPLLPYHHSSASVPASTLITSHHHFYLTITLCQCSCLNTHHLSSSLLPYHHSSASVPASTHITSHHHFYLTITSLPVFLPQHTSPLITTSPYHH
# FSASTCSLPYLTRPDLF]
# end gene g1
###
# start gene g2
scaffold_3119	AUGUSTUS	gene	17555	29618	0.01	-	.	g2
scaffold_3119	AUGUSTUS	transcript	17555	29618	0.01	-	.	g2.t1
scaffold_3119	AUGUSTUS	tts	17555	17555	.	-	.	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	exon	17555	18304	.	-	.	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	stop_codon	18239	18241	.	-	0	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	intron	18305	18398	0.98	-	.	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	intron	18578	20232	0.97	-	.	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	intron	20453	22358	0.65	-	.	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	intron	22537	24451	0.1	-	.	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	intron	24616	29618	0.04	-	.	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	CDS	18239	18304	0.98	-	0	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	CDS	18399	18577	0.97	-	2	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	exon	18399	18577	.	-	.	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	CDS	20233	20452	0.98	-	0	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	exon	20233	20452	.	-	.	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	CDS	22359	22536	0.1	-	1	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	exon	22359	22536	.	-	.	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	CDS	24452	24615	0.04	-	0	transcript_id "g2.t1"; gene_id "g2";
scaffold_3119	AUGUSTUS	exon	24452	24615	.	-	.	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [gaatttgtcgctgcgttgaggggagtgaagaatgccgtagacgacatccaccgggaagtgagcgccatgaacgaggtgt
# gtgtggacatgaagacccgactgcaggccaccaaatcagagacccgacacctcatccaccagaccacctcactccagaaccagagcaacaagctacac
# atgcaggagacggtggcggaggcatttgtgcggtgtttccagctgaccttggaggaggtggcggtcatcaaggggtctggccgggagtcgcccatcac
# gccggagttcttcgccgtcctggacaagacgcagaagatacgcagcaacaccaagtacctcctgcagcctggtggtggaggagtgggtggtggtgcgg
# cgggggtggctggtgcgagggttcctggacgccctgactatcggggggcctggggagcaccgcggcccattgagctgcaggcccatgaccccctacgc
# tacgttggggacatgctggcctgggtgcatcaggcgctcccctctgaacgcgaggctgcccagtccttgtttgggaagtgctccaacctggaccccgc
# cgagcagacccgcagcgccgtggccagcgtgtcggagagtgtgtgtcgccccctcaggacccgcatagagcagatgatcgtgacagaccagcagcggg
# agggaggcaagaaacccgtcatgctgtacaagatcagtaaccttctgagattctaccacaatactataatgcaggaaggtggaaaaatagaaacagga
# aaagagttccagagtttaccagtgaaaatgatgaaagagtaa]
# protein sequence = [EFVAALRGVKNAVDDIHREVSAMNEVCVDMKTRLQATKSETRHLIHQTTSLQNQSNKLHMQETVAEAFVRCFQLTLEE
# VAVIKGSGRESPITPEFFAVLDKTQKIRSNTKYLLQPGGGGVGGGAAGVAGARVPGRPDYRGAWGAPRPIELQAHDPLRYVGDMLAWVHQALPSEREA
# AQSLFGKCSNLDPAEQTRSAVASVSESVCRPLRTRIEQMIVTDQQREGGKKPVMLYKISNLLRFYHNTIMQEGGKIETGKEFQSLPVKMMKE]
# end gene g2
###
# command line:
# /gscratch/srlab/programs/Augustus-3.3.2/bin/augustus --codingseq=1 --proteinprofile=/gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/prfl/EOG091G03P0.prfl --predictionStart=13405  --predictionEnd=29618  --species=fly --progress=true ./tmp/scaffold_3119cbai_genome_v1.01.fasta_145855183_.temp