# 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..17]--> unknown_A (12) <--[0..1]--> unknown_B (25) <--[26..39]--> unknown_D (21) <--[4..6]--> unknown_E (38) <--[2..14]--> unknown_F (71) <--[0..32]--> unknown_G (29) <--[0..2]--> unknown_H (25) <--[1..13]--> unknown_I (13) <--[11..29]--> unknown_J (19) <--[2..20]--> unknown_K (26) <--[0..16]--> unknown_L (23) <--[0..3]--> unknown_M (17) <--[0..15]--> unknown_N (15) <--[2..5]--> unknown_O (21) <--[0..1]--> unknown_P (9) <--[0..4]--> unknown_Q (23) <--[26..205]--> unknown_R (30) <--[3..7]--> unknown_S (12) <--[1..15]--> unknown_T (20) <--[0..4]--> unknown_U (6) <--[0..1]--> unknown_V (18) <--[18..130]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5632620180911_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 = 4570, name = Contig56326) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig56326	AUGUSTUS	gene	885	2189	1	+	.	g1
Contig56326	AUGUSTUS	transcript	885	2189	1	+	.	g1.t1
Contig56326	AUGUSTUS	start_codon	885	887	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig56326	AUGUSTUS	intron	1710	1955	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig56326	AUGUSTUS	CDS	885	1709	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig56326	AUGUSTUS	CDS	1956	2189	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig56326	AUGUSTUS	stop_codon	2187	2189	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggggaaggactattataaaattctaggtatcagcaaaggcgcgtccgatgatgaaattaagaagggctaccgaaaaa
# tggcactcaaatatcatccagataaaaataaatcgccgggagctgaagaaaaattcaaagaaattgcagaagcatacgacgttctaagtgataaaaac
# aaaaaggaaatctacgacaaatatggcgaagaaggactaaagaacggcccacccccgggtagtggattccaaggatccgcgcctggtggcgggaattt
# ccactacgaattccaaggtaatccacgagacacattccgtatgttctttggaggggatgatccgttcgccagctttttcagtggaggcggcgggcctg
# gatttggtggtcctggcccgtctcgtatgttccattttggtggcccccacggtccagaggaaatggatgttgacgatgacccgtatagccatttcggg
# gggcccatgggtggtggaggacgaccacagagaaaaaggcaggactcagcggtagtgcgcgagctaccagtggcactggaagatatatacaaaggtgc
# cactaaaaaactcaaaattactcgtaaaatgttgaacaatgacggacgtaccacccgaactgaggacaagatcttgacaattgatattaagcccgggt
# ggaagtcgggaacaaagataacattccctaaggaaggtgatcagactcctaacaatataccggctgatgtcatctttgttataaaagacaaaccacac
# agtgtattcacccgggaggctagtgatattcgatacaaggccaaaatttcgctcaaagacgctttgtgtggcaccacgctacaagtcccgacaataga
# cggcaggaaaattcccttgcgtttacgagaagttgtgaaaccccactctgtcaagcggatacaaggcgaaggactaccgatcccgaaacagccaggaa
# aacgcggggacttgatcatagacttcgatgtggtgttcccgaatcagatctcatccacagccaaagaaattctggcagactgcctgcctgcttcataa]
# protein sequence = [MGKDYYKILGISKGASDDEIKKGYRKMALKYHPDKNKSPGAEEKFKEIAEAYDVLSDKNKKEIYDKYGEEGLKNGPPP
# GSGFQGSAPGGGNFHYEFQGNPRDTFRMFFGGDDPFASFFSGGGGPGFGGPGPSRMFHFGGPHGPEEMDVDDDPYSHFGGPMGGGGRPQRKRQDSAVV
# RELPVALEDIYKGATKKLKITRKMLNNDGRTTRTEDKILTIDIKPGWKSGTKITFPKEGDQTPNNIPADVIFVIKDKPHSVFTREASDIRYKAKISLK
# DALCGTTLQVPTIDGRKIPLRLREVVKPHSVKRIQGEGLPIPKQPGKRGDLIIDFDVVFPNQISSTAKEILADCLPAS]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937068H.prfl --predictionStart=0  --predictionEnd=21088  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5632620180911_busco_2432604931_.temp