# 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..2]--> unknown_A (22) <--[7..16]--> unknown_B (33) <--[0..1]--> unknown_C (7) <--[0..1]--> unknown_D (45) <--[9..36]--> unknown_E (43) <--[16..263]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4409020180911_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 = 7802, name = Contig44090) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig44090	AUGUSTUS	gene	531	1247	0.33	-	.	g1
Contig44090	AUGUSTUS	transcript	531	1247	0.33	-	.	g1.t1
Contig44090	AUGUSTUS	stop_codon	531	533	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig44090	AUGUSTUS	CDS	531	1247	0.33	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig44090	AUGUSTUS	start_codon	1245	1247	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtcttttcgggataacaatagctcctctgtgcaagctgtcaatgtgaaccaggtgagggttaagcagaggacaacaa
# ttcctcctaggtcagtggtaagaatctcttgttgtgctgagaccaagttagaacctggatgtttcctcattgaacccagtgtcaacacgatgattgtt
# cctcggatatgttctgtgggtgcaacagatccagtgatggtattcatcaatacatcggatgccaaggtgacattatttagaaatcagaaggtaggaag
# tgtacacagtgttgaagaagttcttcctgatgaaaagaaaggttctaataatgtgtatcagaccaaacgggtaagaaattcaattgaacaagagacag
# tctactacttgtttgataggtcatgtagagaattagacgagaaacatcatcctggtcttaagcaattgcttatagactatcctgatgtgttctcagcg
# cacgagttcgacttggggaactttacgtcaatagagcatgctatagaaacgggagatagtaaacctgttaaaaaaaagttcagacgcacaccagcatc
# ctttgagggtgaagaagagaagcacattcaaaaatgtgaaagccagatgttaagtcgagccgtactatattctgaatgggcatcatccgccagtatta
# ggcgcaaaagagatgggactgtaagatggtgtgtggatatagagcgttaa]
# protein sequence = [MSFRDNNSSSVQAVNVNQVRVKQRTTIPPRSVVRISCCAETKLEPGCFLIEPSVNTMIVPRICSVGATDPVMVFINTS
# DAKVTLFRNQKVGSVHSVEEVLPDEKKGSNNVYQTKRVRNSIEQETVYYLFDRSCRELDEKHHPGLKQLLIDYPDVFSAHEFDLGNFTSIEHAIETGD
# SKPVKKKFRRTPASFEGEEEKHIQKCESQMLSRAVLYSEWASSASIRRKRDGTVRWCVDIER]
# end gene g1
###
# start gene g2
Contig44090	AUGUSTUS	gene	2181	3596	0.56	-	.	g2
Contig44090	AUGUSTUS	transcript	2181	3596	0.56	-	.	g2.t1
Contig44090	AUGUSTUS	stop_codon	2181	2183	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig44090	AUGUSTUS	CDS	2181	3596	0.56	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig44090	AUGUSTUS	start_codon	3594	3596	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgaatcaagcagaggagagagagctgcatataatgagttcagacccgcctatggtgaattcagacctgcctttggtga
# gtcagggcattcaacaagtaagtcagccatcattatctaacatgcatcaaccaacctctaacagtccaatgtggggccaaatgcacaggcctgtgggc
# atgcaaccaccacaggtgtcacgtatgatacaaccaggtacaatgccaccaggtatgacacaactaggtacaatgccaccagttatggcacaaccacg
# catgacacaatcaggtatgcccccaccccagttcatgcccttttatccaggctatccatggatgcagtatgggatgccgtaccccatacccccttatt
# atcagcaaccgatggtgagccctatgcctggtagtcctttaccaaggcaaccacaaaaggtaagtaactgggcatcagtatatgataaccaggtacta
# cctcaattggcagtagccagcaatgggcaactagccaataggaatcaggagccaccacagatggtaggtagaacgctgcctgctataccacagcaaca
# atcatcgctgttgttaagggtgagtgaagatgatagacaacaacgtccagtcagtcagagggacgcggaacctcgttcaaggcgccaacgagtggggg
# aagttgggctaccacgtcttcgactagtggatgacgtgcaaccacgccgtcaactggtcgaggaggagtttccaacgcgccgtcagctggggaacgac
# gtgcaaccacgccgtcaattagctgatgatgtcctaccaccacgtcgtcaaagattgcgagatgaattagaaagaccacgacgtcgccagcgattaga
# cgaggaattaccaccgcaccgccaaagaccggacgatgaacttgagcaacagcgtcctcaaagacatgacattggcgtgaatccgctacccgaccagg
# gccaacaaccccctgtcgagcagtcacgtcatgacgcacttcgccagcagcaggatgcaggcaatcgagggccagtgagaagagaggaaggcttaccg
# aagggacttcgatttgacggtaaggaaaactggctcggatttaagcacaagtccatgcgttactatcaggtgaggcaatggacaccaaatgaggcaag
# atattatttatgttggtgtcttgatggtaaggctagcgagttctatgccacagtagttgcaagaaatcaacaaattggtttcttggaactactaaaca
# agctggaaaagagatttgggagtgttcagctgccggacactgctcaagttcagctgaccaactcaaagcagaagccagaggaaactattgaggattgg
# gcagacagagtattgcagctgtctgttcgtgcattccctgacttaccagaggaatacatgtag]
# protein sequence = [MNQAEERELHIMSSDPPMVNSDLPLVSQGIQQVSQPSLSNMHQPTSNSPMWGQMHRPVGMQPPQVSRMIQPGTMPPGM
# TQLGTMPPVMAQPRMTQSGMPPPQFMPFYPGYPWMQYGMPYPIPPYYQQPMVSPMPGSPLPRQPQKVSNWASVYDNQVLPQLAVASNGQLANRNQEPP
# QMVGRTLPAIPQQQSSLLLRVSEDDRQQRPVSQRDAEPRSRRQRVGEVGLPRLRLVDDVQPRRQLVEEEFPTRRQLGNDVQPRRQLADDVLPPRRQRL
# RDELERPRRRQRLDEELPPHRQRPDDELEQQRPQRHDIGVNPLPDQGQQPPVEQSRHDALRQQQDAGNRGPVRREEGLPKGLRFDGKENWLGFKHKSM
# RYYQVRQWTPNEARYYLCWCLDGKASEFYATVVARNQQIGFLELLNKLEKRFGSVQLPDTAQVQLTNSKQKPEETIEDWADRVLQLSVRAFPDLPEEY
# M]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370RCQ.prfl --predictionStart=0  --predictionEnd=27279  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4409020180911_busco_2432604931_.temp