# 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
# --[3..23]--> unknown_A (33) <--[1..3]--> unknown_B (23) <--[0..1]--> unknown_C (16) <--[0..1]--> unknown_D (19) <--[0..38]--> unknown_E (62) <--[2..21]--> unknown_F (57) <--[0..9]--> unknown_G (11) <--[0..1]--> unknown_H (9) <--[0..4]--> unknown_I (7) <--[0..1]--> unknown_J (6) <--[0..2]--> unknown_K (8) <--[0..17]--> unknown_L (14) <--[0..1]--> unknown_M (16) <--[1..3]--> unknown_N (12) <--[0..1]--> unknown_O (22) <--[6..23]--> unknown_P (8) <--[9..99]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_2847cbai_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 = 6082, name = contig_2847) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
contig_2847	AUGUSTUS	gene	1516	3330	0.04	+	.	g1
contig_2847	AUGUSTUS	transcript	1516	3330	0.04	+	.	g1.t1
contig_2847	AUGUSTUS	exon	1516	2248	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2847	AUGUSTUS	start_codon	1847	1849	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_2847	AUGUSTUS	intron	2249	2355	0.99	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2847	AUGUSTUS	CDS	1847	2248	0.81	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_2847	AUGUSTUS	CDS	2356	3204	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_2847	AUGUSTUS	exon	2356	3330	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_2847	AUGUSTUS	stop_codon	3202	3204	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_2847	AUGUSTUS	tts	3330	3330	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcagacctcacggaaatattcctgcagggtgaaaacttcctacgccctcaggtggccgacgagcgtccaccttcacg
# gcgaggcagcaggcggctgcttcggctgtttcaggaagaccttcgtgccggtggcgtgcatcaccgtgccgcccgacacgtggcagatgctccccggg
# cacacgtgggaacacgagaagtgggtaaacacggaggccgagctccgcatcgacttcgggaagctggacgccatggacggcacgggacgtcgcctgaa
# ggtgaaggcgaagcgcgggcagaagaccattgccaagggcaccttcgcaaacatcttcgacaacgttgaagatggcgactttgcgtttggtattgcgt
# ttggcaaggatggcttatcgctgtccttgagggaggggaacaaaatggatgtacttccacccccgtcgatgtattatgaagaagaaagcagcgacgag
# gagaatgtccaggatgacggattctgtgacatttctcttgacgacacaagtgacgacgacggcaacggcctctcgtctccgctggttgagacaagcga
# cagtctcaaccagcagcttcagttgccgaccttctccatggtgcccgagacacccttgcctggacgtcaggacagcctcatgccctcgctgcccgccc
# tgctgtggttcgccaaccaggcagtggccgtggcggcaccggctgtgtgcgtgtacggcgcggtggtgccactgctggaagacaccgtgcccttcctg
# gctggcctgtcctcgcgccctgatgaggtgacgagcgtggtgcaggcggcgtgcgtggccttcgtgctggtcacgacaggctattggtacgctgccct
# ggtggcgcggccctcctgcaggcggcggcacaggcagcgggataagtactgtgcggcctgcgaggaggaggtgccggtggacgagtggcactgcgagg
# tgtgcggcgagtgcgtggagggcagacagcaccactcggtgctgctgaaccggtgcgtgggtgccgccaacgtggcgctttacaggacgctgatgaag
# ctcctgaccactggcgccgcggcggtgctggtgctgttcctcctggaggcggtgatgggccagccgtggcgcctcctccaggtcgggctgttgttgtg
# ctgtgccctgggctcggcacactgccgcaacgccgcggccaaagagcgagccaggcaggcttgtcgcggtgactggtccctgctcgaggagtga]
# protein sequence = [MQTSRKYSCRVKTSYALRWPTSVHLHGEAAGGCFGCFRKTFVPVACITVPPDTWQMLPGHTWEHEKWVNTEAELRIDF
# GKLDAMDGTGRRLKVKAKRGQKTIAKGTFANIFDNVEDGDFAFGIAFGKDGLSLSLREGNKMDVLPPPSMYYEEESSDEENVQDDGFCDISLDDTSDD
# DGNGLSSPLVETSDSLNQQLQLPTFSMVPETPLPGRQDSLMPSLPALLWFANQAVAVAAPAVCVYGAVVPLLEDTVPFLAGLSSRPDEVTSVVQAACV
# AFVLVTTGYWYAALVARPSCRRRHRQRDKYCAACEEEVPVDEWHCEVCGECVEGRQHHSVLLNRCVGAANVALYRTLMKLLTTGAAAVLVLFLLEAVM
# GQPWRLLQVGLLLCCALGSAHCRNAAAKERARQACRGDWSLLEE]
# end gene g1
###
# start gene g2
contig_2847	AUGUSTUS	gene	3526	5576	0.03	+	.	g2
contig_2847	AUGUSTUS	transcript	3526	5576	0.03	+	.	g2.t1
contig_2847	AUGUSTUS	tss	3526	3526	.	+	.	transcript_id "g2.t1"; gene_id "g2";
contig_2847	AUGUSTUS	exon	3526	5576	.	+	.	transcript_id "g2.t1"; gene_id "g2";
contig_2847	AUGUSTUS	start_codon	4665	4667	.	+	0	transcript_id "g2.t1"; gene_id "g2";
contig_2847	AUGUSTUS	CDS	4665	4868	0.82	+	0	transcript_id "g2.t1"; gene_id "g2";
contig_2847	AUGUSTUS	stop_codon	4866	4868	.	+	0	transcript_id "g2.t1"; gene_id "g2";
contig_2847	AUGUSTUS	tts	5576	5576	.	+	.	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgatgatgataataatgataatgatgaaaagaatagtgataatgataataaggatccatttagtgttcaataaagata
# gaaagcttgatatcttctttacatctctcgatcatcgctttaaggactggctgctaagggtttttattgtgaggcttatgacttttattatgcccctg
# gccagtccgttgcgcatgtcaggatga]
# protein sequence = [MMMIIMIMMKRIVIMIIRIHLVFNKDRKLDIFFTSLDHRFKDWLLRVFIVRLMTFIMPLASPLRMSG]
# 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/EOG091G0HOK.prfl --predictionStart=0  --predictionEnd=8051  --species=fly --progress=true ./tmp/contig_2847cbai_genome_v1.01.fasta_145855183_.temp