# 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
# --[4..59]--> unknown_A (48) <--[1..17]--> unknown_B (20) <--[4..23]--> unknown_C (15) <--[57..209]--> unknown_F (22) <--[0..1]--> unknown_G (29) <--[6..29]--> unknown_H (17) <--[10..64]--> unknown_J (77) <--[11..38]--> unknown_K (19) <--[2..116]--> unknown_L (15) <--[12..23]--> unknown_N (29) <--[3..9]--> unknown_O (23) <--[4..22]--> unknown_P (10) <--[2..4]--> unknown_Q (12) <--[3..110]--> unknown_R (15) <--[0..1]--> unknown_S (33) <--[0..87]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5625820180911_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 = 14453, name = Contig56258) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig56258	AUGUSTUS	gene	817	2464	0.44	-	.	g1
Contig56258	AUGUSTUS	transcript	817	2464	0.44	-	.	g1.t1
Contig56258	AUGUSTUS	stop_codon	817	819	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig56258	AUGUSTUS	intron	1366	2260	0.79	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig56258	AUGUSTUS	CDS	817	1365	0.8	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig56258	AUGUSTUS	CDS	2261	2464	0.44	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig56258	AUGUSTUS	start_codon	2462	2464	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaaaatattgacacttactatggattccagagtggcagaacatgctagggcgacatcagccgcacagagtttgtttt
# tatatccatactgggcgttgtatgaggggatgacgacatcatctgatactaatctaaaagtagatattccacaacatcatagagctgatcagttagga
# aagctgtccaaaacgatcaaaaacattctaattccagactaccctcaaaatcaacacttccacaagcctaatccatccactctgcaaatcaataccta
# ccacaagccctaccacactccctcaaaatcacctaccacaagccgtaatccactccccaaaatcactccaaactctaatccagactccctcaaatcac
# ctacacacagccatcacactacctcaaaaatcatctacatcacaatccaatcagactcctcaaaatctacctacataatgctaatccagactccctca
# aaatcacctaccacagcactaaccagactccctcataacaccagtaccactacagctaatccgacactcccttacaaaatcatctaccacagaccaaa
# ccacactacctctaaaatcacctaccacaagcctaatccacactaccatcaaaaatcaccctaccaacaacctaatccaacacgccctcaaaatcacc
# ctacaaggaacctaacagactccctcaaaatcaacctcaattctaatccaactccaaacatctatataagttatctcacaggataa]
# protein sequence = [MKILTLTMDSRVAEHARATSAAQSLFLYPYWALYEGMTTSSDTNLKVDIPQHHRADQLGKLSKTIKNILIPDYPQNQH
# FHKPNPSTLQINTYHKPYHTPSKSPTTSRNPLPKITPNSNPDSLKSPTHSHHTTSKIIYITIQSDSSKSTYIMLIQTPSKSPTTALTRLPHNTSTTTA
# NPTLPYKIIYHRPNHTTSKITYHKPNPHYHQKSPYQQPNPTRPQNHPTRNLTDSLKINLNSNPTPNIYISYLTG]
# end gene g1
###
# start gene g2
Contig56258	AUGUSTUS	gene	2637	10875	0.03	+	.	g2
Contig56258	AUGUSTUS	transcript	2637	10875	0.03	+	.	g2.t1
Contig56258	AUGUSTUS	start_codon	2637	2639	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig56258	AUGUSTUS	intron	2640	3595	0.34	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig56258	AUGUSTUS	intron	3652	5990	0.44	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig56258	AUGUSTUS	intron	6088	10752	0.58	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig56258	AUGUSTUS	CDS	2637	2639	0.29	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig56258	AUGUSTUS	CDS	3596	3651	0.46	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig56258	AUGUSTUS	CDS	5991	6087	0.64	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig56258	AUGUSTUS	CDS	10753	10875	0.16	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig56258	AUGUSTUS	stop_codon	10873	10875	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggataaaagcaacaatcctacagacaatttcctgaaagcactggatgttttaaataggtctaatgtggattccctag
# aaaaggcaatagatctagcgaggaagcaactgcaagcagtggtcactcaggtccagaccttcctggacatccatcagactcgcaacaaaagagcccgt
# tctctgccattagtgttgggagcccctttggatttggaacaagggacaacattagtcattggtatcccacctctgcagcttgatgaagacaggaaaaa
# gtaa]
# protein sequence = [MDKSNNPTDNFLKALDVLNRSNVDSLEKAIDLARKQLQAVVTQVQTFLDIHQTRNKRARSLPLVLGAPLDLEQGTTLV
# IGIPPLQLDEDRKK]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937084T.prfl --predictionStart=0  --predictionEnd=21768  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5625820180911_busco_2432604931_.temp