# 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..422]--> unknown_A (34) <--[0..1]--> unknown_B (66) <--[1..7]--> unknown_C (42) <--[0..4]--> unknown_D (47) <--[0..0]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3055520180911_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 = 37236, name = Contig30555) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig30555	AUGUSTUS	gene	18551	29283	0.03	+	.	g1
Contig30555	AUGUSTUS	transcript	18551	29283	0.03	+	.	g1.t1
Contig30555	AUGUSTUS	intron	18551	22121	0.21	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	intron	22141	23060	0.28	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	intron	23098	24239	0.54	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	intron	24401	26854	0.81	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	intron	26949	27574	0.22	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	intron	27606	29072	0.12	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	CDS	22122	22140	0.29	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	CDS	23061	23097	0.45	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	CDS	24240	24400	0.96	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	CDS	26855	26948	0.8	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	CDS	27575	27605	0.17	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	CDS	29073	29283	0.38	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig30555	AUGUSTUS	stop_codon	29281	29283	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [caaaatccacgtcattcaagacaggaatattcatggttggcagaaggttgggcaaaatgatgggggctccaacagacaa
# gccaagggagataagaacactgccaaactggatcgtgagactgaagagctccaccatgataccgtcggattggacgtttccaaactgattcagctcgg
# gcgaagtgaaaagaagtttactcaaaaggatctggctacaaaaattaatgaaaaagtccaagttatcacagaatatgagaatggaagagcaattccga
# gccaacaagttttagctaaaatggaaaggattcttgtggtagagcagccgtttttgactgagaggttatgggccttcccctccatcgtttgtgatagg
# cataatacgtcgcccgggacggaagtcagggtgtgccagatagccatcgttgctgcagtcatcagttcagcctcctcacgtcgtctaagaactttctc
# tctccaaaattcagccacaggcttgataattatgatattgtgttctgactatttgaacattcatggcggagcttctcactaa]
# protein sequence = [KIHVIQDRNIHGWQKVGQNDGGSNRQAKGDKNTAKLDRETEELHHDTVGLDVSKLIQLGRSEKKFTQKDLATKINEKV
# QVITEYENGRAIPSQQVLAKMERILVVEQPFLTERLWAFPSIVCDRHNTSPGTEVRVCQIAIVAAVISSASSRRLRTFSLQNSATGLIIMILCSDYLN
# IHGGASH]
# end gene g1
###
# start gene g2
Contig30555	AUGUSTUS	gene	37250	38751	0.18	-	.	g2
Contig30555	AUGUSTUS	transcript	37250	38751	0.18	-	.	g2.t1
Contig30555	AUGUSTUS	stop_codon	37250	37252	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig30555	AUGUSTUS	intron	37436	37930	0.87	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig30555	AUGUSTUS	intron	38037	38695	0.19	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig30555	AUGUSTUS	CDS	37250	37435	0.87	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig30555	AUGUSTUS	CDS	37931	38036	0.5	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig30555	AUGUSTUS	CDS	38696	38751	0.21	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig30555	AUGUSTUS	start_codon	38749	38751	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgtttgaacatgagcaccacaaaaagatgacaacatctgaaatagcagccatgcttaaaggtgtggtgtacagttttg
# accctgtgggatcctatggatcggatggttacagagccaggggatcggcagctgctatgctacagcctctgttagataaccagattgggttgaaaaat
# cagcagaatgtcccaagagtaccactgtcaaaagaaaaagtgattaacctagtaaaggatgtatttatttctgcagcggaacgtgatatttataccgg
# tgacgccgtggtagtccgggtcattaccaaggatggcactaccacggagaggttcccactcaggcgagattaa]
# protein sequence = [MFEHEHHKKMTTSEIAAMLKGVVYSFDPVGSYGSDGYRARGSAAAMLQPLLDNQIGLKNQQNVPRVPLSKEKVINLVK
# DVFISAAERDIYTGDAVVVRVITKDGTTTERFPLRRD]
# end gene g2
###
# start gene g3
Contig30555	AUGUSTUS	gene	45340	47091	0.88	+	.	g3
Contig30555	AUGUSTUS	transcript	45340	47091	0.88	+	.	g3.t1
Contig30555	AUGUSTUS	start_codon	45340	45342	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig30555	AUGUSTUS	intron	45816	46001	1	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig30555	AUGUSTUS	CDS	45340	45815	0.88	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig30555	AUGUSTUS	CDS	46002	47091	1	+	1	transcript_id "g3.t1"; gene_id "g3";
Contig30555	AUGUSTUS	stop_codon	47089	47091	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atggatttttcagacgatgaagaggaactcagcgttcctcaggttaagaaaccattagtatatggaagtctagaggaaa
# gagaaagacagagacttgcaggcggcagcacttcaggatctttagcctcagacgccataaaagcgggtaaagctgcagggaatataaacataacggag
# ggagggtcctatgacattgccgaagtagaccccaacgagggacaagcagaattgctagctgtactagaaaaaaagaagaaagccagacaaattcaggt
# gtcgacggatgactctgaagttaaagccaacctcagacaattaggcgagccaatctgtttgttcggagagggtccagctgacagaagagatcgtctca
# gaagaactttagctgaactgggatcagttgccacagatgcaatattgagaaaggaaaaagaattatcagagaagaaaagtaaagaggaggagaatgtt
# acatggtaccacgaagggacttctgctctgaaagaagcaagagtatggatagcaaaatactccattcctaaagctaaagagagaataaaattacaaag
# agaagagaaactgataccaacagcgaagaaaaatgcccagcttcaagacctgcataaacgagttagagcagtcaccaatgagtgcagtcagattggag
# atgttaggccactttcgtattgtgagtttagtcccaatggtaaaatactggctgtagcatcatggtcaggcttgtgcaagttgtggtctgtcccagat
# tgccagctcattcgacaattaagggggcataactgcaatgttggagccattgtttttcatcctaaagctacacttgcattggatgacaattcatgctg
# tatggcttcctgtagtcaggatgggactgtcaagctctggaatcttgtgagtgatgaaccagtggcagacatagaaggccacagcccatacagagtgt
# ctcgtctgaagtaccacccttcagggcgatttttgggcacctgctgctttgacaactcctggagactttgggatttagaagtccaagaggaaattctt
# catcaggagggccacagtaaaccagtttatgacatctccttccagagggatggtgctttagcagcaacaggagggcttgatgcattcggaagaatttg
# ggatctaagaacggggagatgcatcatgtttttggagggccatatcaagtcagttttttctgttgattttgctcctgatggttatcatgttgcaacag
# gaagtgaagataactcggtgaggatttgggatctaaggcagaggaaatgtgtatacaccattccatctcataagaatttagtgagcaaagtgaagttc
# caaccggatcatggcagttatctaataagtgcatcttatgattgtacatccaaagtctgggcccatccaacatgggcaccattgaaaacattagcagg
# gcatgaaggaaaagtgatgggtgcagacatttctcctgatcttaagtacattgcaacagtatcttatgacagaacattcaaactgtggaccactgaac
# tgcaaggaggaatttaa]
# protein sequence = [MDFSDDEEELSVPQVKKPLVYGSLEERERQRLAGGSTSGSLASDAIKAGKAAGNINITEGGSYDIAEVDPNEGQAELL
# AVLEKKKKARQIQVSTDDSEVKANLRQLGEPICLFGEGPADRRDRLRRTLAELGSVATDAILRKEKELSEKKSKEEENVTWYHEGTSALKEARVWIAK
# YSIPKAKERIKLQREEKLIPTAKKNAQLQDLHKRVRAVTNECSQIGDVRPLSYCEFSPNGKILAVASWSGLCKLWSVPDCQLIRQLRGHNCNVGAIVF
# HPKATLALDDNSCCMASCSQDGTVKLWNLVSDEPVADIEGHSPYRVSRLKYHPSGRFLGTCCFDNSWRLWDLEVQEEILHQEGHSKPVYDISFQRDGA
# LAATGGLDAFGRIWDLRTGRCIMFLEGHIKSVFSVDFAPDGYHVATGSEDNSVRIWDLRQRKCVYTIPSHKNLVSKVKFQPDHGSYLISASYDCTSKV
# WAHPTWAPLKTLAGHEGKVMGADISPDLKYIATVSYDRTFKLWTTELQGGI]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370R3M.prfl --predictionStart=18551  --predictionEnd=58760  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3055520180911_busco_2432604931_.temp