# 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..43]--> unknown_A (11) <--[1..5]--> unknown_B (12) <--[0..2]--> unknown_C (19) <--[7..62]--> unknown_E (10) <--[1..21]--> unknown_F (15) <--[1..15]--> unknown_G (28) <--[1..22]--> unknown_H (22) <--[42..246]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5757620180911_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 = 13045, name = Contig57576) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig57576	AUGUSTUS	gene	7511	9703	1	-	.	g1
Contig57576	AUGUSTUS	transcript	7511	9703	1	-	.	g1.t1
Contig57576	AUGUSTUS	stop_codon	7511	7513	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig57576	AUGUSTUS	CDS	7511	9703	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig57576	AUGUSTUS	start_codon	9701	9703	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcctgcaaagaaaaaccgattcttgcttttatacggatcccagactggacaggcagaggccattacagatgagatcc
# gagagaactcggtcgtgcatggcctggattgtgagagacattgcctcagtcaaatggagaaaaaattcacactcgagaatgagacttgtgtcgtgatt
# gtcacatccactacaggcgatggggaaccaccagacacagctctgaaatttttcaggaggctgaagaagaaaacgcttcctagtgatcatctgtctca
# tatgaattacgctctgttagggctgggggattccaactacacaaatttctgtaatgcggggaagacactggacaggcgaatggaggaattgggagcca
# aacggttctacccctccggctgggctgatgatgctgtaggtctggaaatagcagtggagccatggatagagggactgttcccagcactgcttaaattc
# ctgtcaccagacctttcaattggaaacaattccaatctcagcagtaaagaagaagacactggtgatcttccgaacagtctagattgtgatgttaaaca
# tgacaaaactgaacctaatggtaccacagtaacaatctgccatccatcaaccaatggtcattccaaggcggaacaaggtgaccataatgaacatgata
# ctccttcttcaaaaattgatgggaaaacattagataatggatcagaagattctctggaaagaaagatggagaaaatttcaatagcaaacacacaggaa
# ccatcacttaccaaatcagtgcaacccctgtgtgatgcggctgttacagttcctttactgacacccccttacctcgcactaaaattcaattcagagaa
# aaacgtagaaggcacctctatcccttttgataaaactgctgcaacggtgatttccaaggcctcggtaatcggtgcagatattctaacttcagaagatg
# cgctgaagaaatctctaaaattgagacttgagttagaaaatgagatgaagtacctaccaggagattctgtgtcagtgtactgccagaatgatgcaata
# gaggtggaaatgctgctgaagagactgaatgttcaggacactgcagactgtgtgtgtgagattgagcttatgaaagacaccaagaaagcaaaagcagt
# tttcccgctgcatctgccctctgtctccacactcaggaacttgttcactcactacatagacataagggtacctcccaaaaaatctgtgatacgacaac
# ttgtggaagaaaccacgaatccacaagagaaaagaagacttcaagagttgtgcagcaagcaaggcatggcggactacaccagctttataaggaaccct
# gggataggtatactagatctcctccaggcgtttccctcctgtcagccgactgttgacagattgatagagtcgcttccaaagctacaaccaaggccgta
# ctccgcgtgtagttcaccgcttaaaacaccaaaccagttagacattgtgttcaatgtgatcaatataccagagggggacggaagaagcttttcaagac
# aaggggtatgcactggaatgctagataaattgacagtaggtattcagagcggacagaaagatgaagattcaaagaaagatggaggaccagatgggaaa
# atctgccagctgtatgtgtcggccaggcccaatcagtccttccatttacccgatgacgtgcgtctgccgctcatcatggtgggaccaggcacaggagt
# ggctccctttgtcgggttcttacaacacagagaaatgcagaaaaccctgcctgaatatgcagaccaggtgttcggagaaaccttcctattctttggtt
# gtagaaaccaatcacaagactttttattcagggaggaacttctgaggttacaagaggttaaaattttgacaaagctcttcgtttccttctctcgtgaa
# agtaagtctgcagatgagcctaaatatgtacaagacaatctgatgaaaattgccgagttagtacttgatttgattgagaaacaagaagcagtaatata
# tgtgtgtggtgatgccaagaatatgtccaaagatgtgaatcaggctttcatgacaattctgaaggaaaagaaaggaatgagtgaaagtgaggctaagt
# cccatgttaccaaactgaggctcaataggaggtacctggaggatgtgtggacctag]
# protein sequence = [MPAKKNRFLLLYGSQTGQAEAITDEIRENSVVHGLDCERHCLSQMEKKFTLENETCVVIVTSTTGDGEPPDTALKFFR
# RLKKKTLPSDHLSHMNYALLGLGDSNYTNFCNAGKTLDRRMEELGAKRFYPSGWADDAVGLEIAVEPWIEGLFPALLKFLSPDLSIGNNSNLSSKEED
# TGDLPNSLDCDVKHDKTEPNGTTVTICHPSTNGHSKAEQGDHNEHDTPSSKIDGKTLDNGSEDSLERKMEKISIANTQEPSLTKSVQPLCDAAVTVPL
# LTPPYLALKFNSEKNVEGTSIPFDKTAATVISKASVIGADILTSEDALKKSLKLRLELENEMKYLPGDSVSVYCQNDAIEVEMLLKRLNVQDTADCVC
# EIELMKDTKKAKAVFPLHLPSVSTLRNLFTHYIDIRVPPKKSVIRQLVEETTNPQEKRRLQELCSKQGMADYTSFIRNPGIGILDLLQAFPSCQPTVD
# RLIESLPKLQPRPYSACSSPLKTPNQLDIVFNVINIPEGDGRSFSRQGVCTGMLDKLTVGIQSGQKDEDSKKDGGPDGKICQLYVSARPNQSFHLPDD
# VRLPLIMVGPGTGVAPFVGFLQHREMQKTLPEYADQVFGETFLFFGCRNQSQDFLFREELLRLQEVKILTKLFVSFSRESKSADEPKYVQDNLMKIAE
# LVLDLIEKQEAVIYVCGDAKNMSKDVNQAFMTILKEKKGMSESEAKSHVTKLRLNRRYLEDVWT]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370TS7.prfl --predictionStart=0  --predictionEnd=21594  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5757620180911_busco_2432604931_.temp