# 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..59]--> unknown_A (10) <--[9..41]--> unknown_B (12) <--[1..2]--> unknown_C (16) <--[0..13]--> unknown_D (20) <--[0..1]--> unknown_E (20) <--[0..4]--> unknown_F (22) <--[0..9]--> unknown_G (20) <--[0..2]--> unknown_H (38) <--[0..13]--> unknown_I (28) <--[0..4]--> unknown_J (6) <--[0..3]--> unknown_K (92) <--[0..1]--> unknown_L (25) <--[1..18]--> unknown_M (64) <--[0..1]--> unknown_N (16) <--[4..100]--> unknown_O (21) <--[0..155]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5954120180911_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 = 18201, name = Contig59541) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig59541	AUGUSTUS	gene	217	7657	0.03	-	.	g1
Contig59541	AUGUSTUS	transcript	217	7657	0.03	-	.	g1.t1
Contig59541	AUGUSTUS	stop_codon	217	219	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	intron	401	1179	0.45	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	intron	1200	1651	0.49	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	intron	1757	2359	0.92	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	intron	2528	4162	0.85	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	intron	4290	5810	0.41	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	intron	5840	7417	0.25	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	CDS	217	400	0.6	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	CDS	1180	1199	0.49	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	CDS	1652	1756	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	CDS	2360	2527	0.81	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	CDS	4163	4289	0.68	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	CDS	5811	5839	0.58	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	CDS	7418	7657	0.3	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig59541	AUGUSTUS	start_codon	7655	7657	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtctgagagaaacataaatgcaatagtgattagagcaggaaaggctctaccaaaaattgtaaatatggcggtctcga
# ccccaggcggccaaaacttgatacatacagtccctgaaacgtattactttaccattactttccgtgcgtctgcgtgcggtaccgtcacagtctttgcg
# gcagcgtgcgtcaccagttcagcggtcagcggttaccgaatagccgagcagcggatcggtcacaaattacagccaaatccggagagtaacagaaacgc
# taggattacacactattttactgcgaagatattaagtccaagtactaacacgataaaagccaaagaggtcggcgaatggtgctccagatttggtaagg
# agctctcccctcagatggaatcgatggaacttctgcaaaatttttatgaaacaacactagatgccctcaaggaagccaaaaatgagagactgtggttt
# aaaaccaataccaagctaggcaagctgtacttcgaccggggcgactaccagaagctacagaagatactcaaacagctacaccagtcctgtcagacgga
# cgatggtgaagatgatctgaagaaaggtacacaactgctggaaatatatgcactggaaattcagatgtacacagcccagaaaaacaacaaaaaactaa
# agttggccataacttttgaatggtcagcgtggcggtcaccagttcgcggtagcgttaccgaaggcgagtcgcggtcggtcacgtgcggtcagcggatc
# aggctttttaggccgctgagtaaactcgaggtgactattgcaatgtctcggatacatcgtcgtcgatgcgtcgatcgtcgtcccgttaacaagcggtt
# ggacttttaa]
# protein sequence = [MSERNINAIVIRAGKALPKIVNMAVSTPGGQNLIHTVPETYYFTITFRASACGTVTVFAAACVTSSAVSGYRIAEQRI
# GHKLQPNPESNRNARITHYFTAKILSPSTNTIKAKEVGEWCSRFGKELSPQMESMELLQNFYETTLDALKEAKNERLWFKTNTKLGKLYFDRGDYQKL
# QKILKQLHQSCQTDDGEDDLKKGTQLLEIYALEIQMYTAQKNNKKLKLAITFEWSAWRSPVRGSVTEGESRSVTCGQRIRLFRPLSKLEVTIAMSRIH
# RRRCVDRRPVNKRLDF]
# end gene g1
###
# start gene g2
Contig59541	AUGUSTUS	gene	11543	15262	0.12	-	.	g2
Contig59541	AUGUSTUS	transcript	11543	15262	0.12	-	.	g2.t1
Contig59541	AUGUSTUS	stop_codon	11543	11545	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig59541	AUGUSTUS	intron	11750	13023	0.25	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig59541	AUGUSTUS	intron	13138	15217	0.58	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig59541	AUGUSTUS	CDS	11543	11749	0.68	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig59541	AUGUSTUS	CDS	13024	13137	0.61	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig59541	AUGUSTUS	CDS	15218	15262	0.58	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig59541	AUGUSTUS	start_codon	15260	15262	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgtcggacgatgagtgcatgtacgatgacgaggagtatgacttggagtactcagaggaaagtaactcggaaccagatg
# ttgacctagaaaatcagtactacaattctaaagccctcaaagaggacgacccacggggcgccctggaaagttttcagaaggggaatttcccagagatg
# atgaaacgatacaagcaattactgatgtacatcaaatcagctgtcaccaggaactactcagaaaagtccatcaactccattctggattacatctccac
# atccaaacaggtttcttataagttaataaaactatggccattaatccaaagattgaagctggtgaaattagagattgttcagtatatttga]
# protein sequence = [MSDDECMYDDEEYDLEYSEESNSEPDVDLENQYYNSKALKEDDPRGALESFQKGNFPEMMKRYKQLLMYIKSAVTRNY
# SEKSINSILDYISTSKQVSYKLIKLWPLIQRLKLVKLEIVQYI]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370CRF.prfl --predictionStart=0  --predictionEnd=33116  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5954120180911_busco_2432604931_.temp