# 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
# --[2..45]--> unknown_A (26) <--[0..22]--> unknown_B (7) <--[0..2]--> unknown_C (17) <--[6..8]--> unknown_D (13) <--[14..49]--> unknown_F (19) <--[0..3]--> unknown_G (68) <--[11..40]--> unknown_H (56) <--[0..26]--> unknown_I (21) <--[35..198]--> unknown_K (13) <--[2..18]--> unknown_L (36) <--[10..16]--> unknown_M (22) <--[30..449]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3941420180911_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 = 29360, name = Contig39414) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig39414	AUGUSTUS	gene	3502	10473	0.06	-	.	g1
Contig39414	AUGUSTUS	transcript	3502	10473	0.06	-	.	g1.t1
Contig39414	AUGUSTUS	stop_codon	3502	3504	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	intron	3678	5503	0.56	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	intron	5595	6541	0.77	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	intron	6605	8221	0.47	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	intron	8229	8858	0.47	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	intron	8993	9124	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	intron	9148	9423	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	intron	9600	10342	0.81	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	3502	3677	0.38	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	5504	5594	0.76	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	6542	6604	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	8222	8228	0.47	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	8859	8992	0.97	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	9125	9147	0.99	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	9424	9599	0.88	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	CDS	10343	10473	0.8	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig39414	AUGUSTUS	start_codon	10471	10473	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcctcctgtaacaatgaagttacccacagagaatcagaacaagacggacgaagagcttgcagtggctaaacctgtga
# ttgggatcatctatccaccaccggaagtcaggagtatccttcaattcttccacatacaaatagacattgtagacaagactgccagttttgttgcaagg
# aatggaccggaatttgaaagtcgtattcgtaaaaatgaaatgaacaatgccaagtttaactttctgaatccctcggatccttaccatgcttactatca
# acataaagtcagagaattcaaggaggggcgtggatcagaaccagtggcaccaaagccagtacctggtgcacccttttcacagaagccagctgagcagg
# ctaaaataatacaagaaataattatccctaaggagcccccaccagaatttgagtttgttgctgaccctccatccatatccgcgtttgattttagcagt
# atccttattcctccaaaggacctgttggataaattacagaaggagtcatttgattacaaagatgtcttgaatcaagtaaaataccgagtagaatggca
# gcggcatcaggatcgggagaagagaaaggaagaagaagccattgaacgggaaagaggacatggaggaaggtctatgaagagggagattgccggtacca
# gaaggaaggcacctaatccccctcaacagccccctcctccccctggaaaagtagaaggggtcccccacccccagggatcatctcccgcctctgcctcc
# caaaactccagaccagtcatgcatccgtcaaattaa]
# protein sequence = [MPPVTMKLPTENQNKTDEELAVAKPVIGIIYPPPEVRSILQFFHIQIDIVDKTASFVARNGPEFESRIRKNEMNNAKF
# NFLNPSDPYHAYYQHKVREFKEGRGSEPVAPKPVPGAPFSQKPAEQAKIIQEIIIPKEPPPEFEFVADPPSISAFDFSSILIPPKDLLDKLQKESFDY
# KDVLNQVKYRVEWQRHQDREKRKEEEAIERERGHGGRSMKREIAGTRRKAPNPPQQPPPPPGKVEGVPHPQGSSPASASQNSRPVMHPSN]
# end gene g1
###
# start gene g2
Contig39414	AUGUSTUS	gene	18364	18877	0.19	-	.	g2
Contig39414	AUGUSTUS	transcript	18364	18877	0.19	-	.	g2.t1
Contig39414	AUGUSTUS	stop_codon	18364	18366	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig39414	AUGUSTUS	intron	18543	18618	0.84	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig39414	AUGUSTUS	CDS	18364	18542	0.93	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig39414	AUGUSTUS	CDS	18619	18877	0.19	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig39414	AUGUSTUS	start_codon	18875	18877	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgatggctactaccaaagccggtcgcgtcctgcagctcaagaatgcttatcgatcaacagactattgggatctgattt
# cccttcgtagtaaactgtcaatcaagtatgtcactgctcaggatctgagggacatgggtgtgactgtggtccccattccttacccagtctcctcgaac
# tctgtgcaagggagaatggtcaatcaagacctggatttatctcaaggattagctggatcactttatgaccctcaaagaaccaggaacctggatgatgt
# gaaagtagaagtagaggtcaaatcacagagcaatgagactccatctgagattacaagtgtgaagaaggaggtgacatctttggggaccagtttagtga
# tcgatttgtgtgacgcagatgaagaaacggaatcggcagttaacaacattattgagttggattaa]
# protein sequence = [MMATTKAGRVLQLKNAYRSTDYWDLISLRSKLSIKYVTAQDLRDMGVTVVPIPYPVSSNSVQGRMVNQDLDLSQGLAG
# SLYDPQRTRNLDDVKVEVEVKSQSNETPSEITSVKKEVTSLGTSLVIDLCDADEETESAVNNIIELD]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370SYK.prfl --predictionStart=0  --predictionEnd=29589  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3941420180911_busco_2432604931_.temp