# 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..6]--> unknown_A (16) <--[0..14]--> unknown_B (22) <--[0..5]--> unknown_C (12) <--[0..4]--> unknown_D (50) <--[0..22]--> unknown_E (61) <--[9..17]--> unknown_G (12) <--[1..21]--> unknown_H (71) <--[2..19]--> unknown_I (23) <--[3..17]--> unknown_J (189) <--[0..1]--> unknown_K (19) <--[0..22]--> unknown_L (15) <--[1..37]--> unknown_M (47) <--[1..7]--> unknown_N (57) <--[0..12]--> unknown_O (36) <--[0..1]--> unknown_P (35) <--[0..7]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig6804820180911_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 = 15476, name = Contig68048) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig68048	AUGUSTUS	gene	4206	9179	0.13	-	.	g1
Contig68048	AUGUSTUS	transcript	4206	9179	0.13	-	.	g1.t1
Contig68048	AUGUSTUS	stop_codon	4206	4208	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	intron	4308	5171	0.76	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	intron	5300	6085	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	intron	6229	6569	0.67	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	intron	6699	6788	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	intron	6905	7261	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	intron	7439	7924	0.75	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	intron	8084	8343	0.92	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	intron	8525	8686	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	intron	8947	9101	0.87	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	CDS	4206	4307	0.58	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	CDS	5172	5299	0.97	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	CDS	6086	6228	0.68	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	CDS	6570	6698	1	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	CDS	6789	6904	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	CDS	7262	7438	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	CDS	7925	8083	0.75	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	CDS	8344	8524	0.92	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	CDS	8687	8946	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	CDS	9102	9179	0.45	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig68048	AUGUSTUS	start_codon	9177	9179	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtgtgataaagtcgtacctggtaacagagtgacagtggtgggaatatattccatcaaaaagacgggaaaacccacaa
# aaggaggcggcagagacaaagtgaatgttggaatccgaagcccctatttcagggtcctgggaatccaggtggacaatgatgggacggggagaggaggg
# gcagcccccatcagccccgcggacgaagaagagttcagaagaatggctaacgatcctaacatctatgaaactatagccaaaagtattgcaccttctat
# ttatggtagtctggatatcaaaaaggctatttcctgtctcttatttggagggtctagaaagagactcccggacggtttgatgagaagaggtgatgtga
# atctcctgatgttaggagaccccggtactgccaaatctcagctcctgaagttcgtggagaggtgctcacctattggtgtgtacacatctggcaaggga
# agtagtgcagcgggtctaacggcatccgtcattagagatccacaaacgaggaactttgtgatggagggaggagctatggtattagccgatggtggagt
# ggtgtgtattgatgagtttgacaaaatgagggaagatgacagagtggctattcacgaggcgatggaacagcagactatatcaatcgcaaaggtattgg
# agtataatcttgctggaatcacgacaacattgaactcgaggtgctcagtgctggctgctgctaacagtgtgtatggtcgttgggatgagaccaaggga
# ggagaaaacatcgactttatgcccaccattttgtctcgatttgatatgatatttattgtaaaagatgaacataatgaagccagagatatgactttggc
# gaagcatgtcatgaatgtgcacttaaatgctctccaaatgacagaggaacacgcagaaggggaaattgacctaaatactctgaagaagttcattcagt
# attgtagaacgaaatgcggcccccgtttgtctcctgaagcagcagagaaactgaagaatagatatgttttgatgaggaatggagcgggtgaatacgaa
# aaggaaacgggcaaaaagataaccattcccatcactgtcaggcaattggaagccatcatcagaatgtctgaatctttggccaagatgaagctgaaacc
# atttgcatcagaaagggaggtggatgaagccctgagattgttccaggtgtccacattagatgctgccatgtctggcaatctgtctggcgtcgaaggat
# ttaccacagaagaggatcaagagctgttatctaggatagagaagcagatcaaaaggcgatttattattggatctcaagtatcagaacatgcgatcatt
# caggacttcacaagacagaagtaccccgagagatccattcagaaagtcttgcatttcatgttgagaagaggagagattcagcaccgtatgcagaggaa
# aatgctgtatcgggtgaaatga]
# protein sequence = [MCDKVVPGNRVTVVGIYSIKKTGKPTKGGGRDKVNVGIRSPYFRVLGIQVDNDGTGRGGAAPISPADEEEFRRMANDP
# NIYETIAKSIAPSIYGSLDIKKAISCLLFGGSRKRLPDGLMRRGDVNLLMLGDPGTAKSQLLKFVERCSPIGVYTSGKGSSAAGLTASVIRDPQTRNF
# VMEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKVLEYNLAGITTTLNSRCSVLAAANSVYGRWDETKGGENIDFMPTILSRFDMIFI
# VKDEHNEARDMTLAKHVMNVHLNALQMTEEHAEGEIDLNTLKKFIQYCRTKCGPRLSPEAAEKLKNRYVLMRNGAGEYEKETGKKITIPITVRQLEAI
# IRMSESLAKMKLKPFASEREVDEALRLFQVSTLDAAMSGNLSGVEGFTTEEDQELLSRIEKQIKRRFIIGSQVSEHAIIQDFTRQKYPERSIQKVLHF
# MLRRGEIQHRMQRKMLYRVK]
# end gene g1
###
# start gene g2
Contig68048	AUGUSTUS	gene	9558	12157	0.5	+	.	g2
Contig68048	AUGUSTUS	transcript	9558	12157	0.5	+	.	g2.t1
Contig68048	AUGUSTUS	start_codon	9558	9560	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig68048	AUGUSTUS	intron	9916	11241	0.84	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig68048	AUGUSTUS	intron	11346	12079	0.53	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig68048	AUGUSTUS	CDS	9558	9915	0.94	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig68048	AUGUSTUS	CDS	11242	11345	0.66	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig68048	AUGUSTUS	CDS	12080	12157	0.53	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig68048	AUGUSTUS	stop_codon	12155	12157	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgacaatggaagcacgtccatccttggtgtcgtacgagaccttactaacacagtccattctctgcaaactagccttgt
# ctcgctcacgaaagagtcaataccctgacaaggcaaagagaaacccttccgccgccgcagggagtccggaacaactaatgggttcttactttaccccg
# acccgtgcgcaacaacaattctacttcgatttcgaatggacgaggatttcacgctacttactgcgtacaacagaccggccgaaacacagtgaagtgta
# caaaaaactcgctatggatatcggcaaatccttgccatttgtggagacaatatctccaactttgaggaagcaaattgttgaagatgacttcttgacaa
# ttgaccatccagactttgcagcccaaactactatggactcactgaccaatatgtttgagcttcttggaattcctttggcaactcacaaaatgagaaaa
# attcgaagactcgcacggaagcagacaggaaaccagtaccactcccccttggacgagatcacactgtga]
# protein sequence = [MTMEARPSLVSYETLLTQSILCKLALSRSRKSQYPDKAKRNPSAAAGSPEQLMGSYFTPTRAQQQFYFDFEWTRISRY
# LLRTTDRPKHSEVYKKLAMDIGKSLPFVETISPTLRKQIVEDDFLTIDHPDFAAQTTMDSLTNMFELLGIPLATHKMRKIRRLARKQTGNQYHSPLDE
# ITL]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093704J7.prfl --predictionStart=0  --predictionEnd=28928  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig6804820180911_busco_2432604931_.temp