# 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..93]--> unknown_A (138) <--[10..63]--> unknown_B (16) <--[0..21]--> unknown_C (68) <--[11..60]--> unknown_D (21) <--[0..1]--> unknown_E (109) <--[0..2]--> unknown_F (108) <--[0..1]--> unknown_G (10) <--[10..20]--> unknown_H (7) <--[5..12]--> unknown_I (20) <--[0..18]--> unknown_J (14) <--[0..3]--> unknown_K (10) <--[4..5]--> unknown_L (20) <--[0..2]--> unknown_M (10) <--[8..20]--> unknown_O (10) <--[0..1]--> unknown_P (6) <--[0..334]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_2844cbai_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 = 6641, name = contig_2844) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
contig_2844	AUGUSTUS	gene	4446	6640	0.02	+	.	g1
contig_2844	AUGUSTUS	transcript	4446	6640	0.02	+	.	g1.t1
contig_2844	AUGUSTUS	tss	4446	4446	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2844	AUGUSTUS	exon	4446	4816	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2844	AUGUSTUS	start_codon	4619	4621	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_2844	AUGUSTUS	intron	4817	5011	0.52	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2844	AUGUSTUS	intron	5155	5239	0.75	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2844	AUGUSTUS	CDS	4619	4816	0.37	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_2844	AUGUSTUS	CDS	5012	5154	0.66	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_2844	AUGUSTUS	exon	5012	5154	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2844	AUGUSTUS	CDS	5240	5951	0.74	+	1	transcript_id "g1.t1"; gene_id "g1";
contig_2844	AUGUSTUS	exon	5240	6640	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2844	AUGUSTUS	stop_codon	5949	5951	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_2844	AUGUSTUS	tts	6640	6640	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgatgaagccgcgggagctgcacaagatccggccgcaccagcaggacgccgtggcctccctggtggacgacgaagcca
# acaccttcctaagcgggtgtgtcgtgttgccctgcgggagtggcaagacgcttgtgggtgtgctgtgcgccagcctcatgcggcgccgcacactggtg
# gtgtgcgtcacgatggagcagacttacggcctgctactcatggacgaggtgcacaggctgcctgccaccgtgtatcgcaatcttcctcaacgcatcaa
# gagcagttggcgggtgggcctcactgccgacctttcccgcgaggcagatgacgatcatataatcttgtggcggcaccactacctcgtggcttctcgca
# tgttatcaaagcgcacaccgggacgcgacgacctccaccgactacttattctactcaacccttacaagttttgttatctgcgttcgctgattcatttt
# gtggaatataaacagcgtcagaagctgcttgttatgtttgaggagctgttgcatctgcaggtgtttgcggtggcgtgcaggcgtccctacgtgagcgg
# taataacgaggcacgagagtccatcgtgcagaactttcagcattctactggaccccaaacactgttagtgagccgcatcggcgatacggggctggacg
# tgcctgatttggcttactgcctgcagctgggcggcttgggtgcttcccgtcagcaagaagtccagcgggtgggacgcgttcagcggctcaagccagat
# gggcgcacttctgagttccattcggtggtaactgtggggccgaagtgttccgagctggagtacagccggcgccgcaacacccacctcgtggagcaagg
# ctaccgcctgcaccagatgccagccaacatagtcctggactccattcccgcctgccagaacgtaaagctagctaagtttgctcggatgctcgctcaca
# aactttctacgggatgcaaggataatgtgaacaagtggatcctcgaggtgtatccaagcttgctgcgttcactcccttaccgcgacctgtga]
# protein sequence = [MMKPRELHKIRPHQQDAVASLVDDEANTFLSGCVVLPCGSGKTLVGVLCASLMRRRTLVVCVTMEQTYGLLLMDEVHR
# LPATVYRNLPQRIKSSWRVGLTADLSREADDDHIILWRHHYLVASRMLSKRTPGRDDLHRLLILLNPYKFCYLRSLIHFVEYKQRQKLLVMFEELLHL
# QVFAVACRRPYVSGNNEARESIVQNFQHSTGPQTLLVSRIGDTGLDVPDLAYCLQLGGLGASRQQEVQRVGRVQRLKPDGRTSEFHSVVTVGPKCSEL
# EYSRRRNTHLVEQGYRLHQMPANIVLDSIPACQNVKLAKFARMLAHKLSTGCKDNVNKWILEVYPSLLRSLPYRDL]
# 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/EOG091G0291.prfl --predictionStart=0  --predictionEnd=10765  --species=fly --progress=true ./tmp/contig_2844cbai_genome_v1.01.fasta_145855183_.temp