# 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 /augustus/config/ ...
# Using protein profile unknown
# --[0..20]--> unknown_A (27) <--[5..8]--> unknown_B (37) <--[0..2]--> unknown_C (29) <--[7..40]--> unknown_D (89) <--[4..17]--> unknown_E (51) <--[0..4]--> unknown_F (41) <--[2..25]--> unknown_G (18) <--[10..27]--> unknown_H (11) <--[0..8]--> unknown_I (13) <--[6..9]--> unknown_K (9) <--[0..3]--> unknown_L (19) <--[2..59]--> unknown_M (36) <--[8..15]--> unknown_N (32) <--[0..34]--> unknown_O (30) <--[3..8]--> unknown_P (47) <--[0..3]--> unknown_Q (47) <--[0..13]--> unknown_R (145) <--[21..677]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2641720180911_busco_2432604931_.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 = 2990, name = Contig26417) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig26417	AUGUSTUS	gene	118	2990	0.37	-	.	g1
Contig26417	AUGUSTUS	transcript	118	2990	0.37	-	.	g1.t1
Contig26417	AUGUSTUS	stop_codon	118	120	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	intron	323	567	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	intron	777	1128	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	intron	1270	1585	0.4	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	intron	1645	1925	0.48	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	intron	2090	2488	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	intron	2626	2990	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	CDS	118	322	0.98	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	CDS	568	776	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	CDS	1129	1269	0.91	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	CDS	1586	1644	0.39	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	CDS	1926	2089	0.5	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig26417	AUGUSTUS	CDS	2489	2625	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gtgaacataaaggccttggaagatgtagtgaggaagtacatcagtctggctgagtctaaaacggaggctgcccgagcgg
# aatcccatcaggctgttgtggacattgatgatctggttgacccagacactccagaaagtctgctgttgaaggcggtcagtggtgaggacacgcaggac
# aggacagatagagccatcctgaccccctgggtcaaatttctgtgggagtcgtacagacagtgcctggacttgctgcgtaataactcgcgcttcgagcg
# actgtaccaggaaatcgcacagcaagctttcaaattttgcttgaagtacaaccggaagaccgagttcagaaagttatgtgacaatttaagaacacatc
# tgggtcacatccacaaacaccagcaccaagcgacggccatcaacctaaacaatcccgagtcgcaggccatgcacttagaaactcgtctggagcagctg
# gacagcgccattaaaatggaactgtggcaggaggcgtttaaggcagtggaagacattcatggcttgattcaactgtccaagaaatctcccaagccttc
# tctgatggccaactactaccagaagctagggatggtgttctggaaatcggggaacggtctcttccatgccagtacgcttcacagactgtacacgttgt
# caagggaacagagaaagaacctctcggcagatgagctacaaaagatggcgtccagggtactttgtgccacgttggccgttcccattccagcctccaga
# aacaccattgaccagctgctggaaatggacgattccacgatggagaagaagcggagattagccactcttctgatgttgaacacccctccctctagaca
# aacgctgatcaaggaattggtaggcaatcttctccctcttctacaaccataa]
# protein sequence = [VNIKALEDVVRKYISLAESKTEAARAESHQAVVDIDDLVDPDTPESLLLKAVSGEDTQDRTDRAILTPWVKFLWESYR
# QCLDLLRNNSRFERLYQEIAQQAFKFCLKYNRKTEFRKLCDNLRTHLGHIHKHQHQATAINLNNPESQAMHLETRLEQLDSAIKMELWQEAFKAVEDI
# HGLIQLSKKSPKPSLMANYYQKLGMVFWKSGNGLFHASTLHRLYTLSREQRKNLSADELQKMASRVLCATLAVPIPASRNTIDQLLEMDDSTMEKKRR
# LATLLMLNTPPSRQTLIKELVGNLLPLLQP]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937036L.prfl --predictionStart=0  --predictionEnd=22091  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2641720180911_busco_2432604931_.temp