# 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..105]--> unknown_A (22) <--[2..17]--> unknown_B (25) <--[0..1]--> unknown_C (28) <--[1..7]--> unknown_D (17) <--[0..4]--> unknown_E (13) <--[0..1]--> unknown_F (37) <--[0..1]--> unknown_G (16) <--[9..80]--> unknown_I (12) <--[0..3]--> unknown_J (23) <--[0..76]--> unknown_K (27) <--[2..110]--> unknown_L (12) <--[7..64]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig10781620180911_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 = 13094, name = Contig107816) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig107816	AUGUSTUS	gene	1	6939	0.01	+	.	g1
Contig107816	AUGUSTUS	transcript	1	6939	0.01	+	.	g1.t1
Contig107816	AUGUSTUS	intron	1	972	0.33	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	intron	1121	1339	0.43	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	intron	1389	1813	0.41	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	intron	1900	2586	0.86	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	intron	2736	2787	0.36	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	intron	2810	3280	0.31	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	intron	3357	4155	0.26	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	intron	4300	4896	0.87	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	intron	4907	5691	0.97	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	intron	5700	5986	0.86	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	intron	6054	6826	0.94	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	CDS	973	1120	0.52	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	CDS	1340	1388	0.45	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	CDS	1814	1899	0.96	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	CDS	2587	2735	0.52	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	CDS	2788	2809	0.36	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	CDS	3281	3356	0.3	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	CDS	4156	4299	0.38	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	CDS	4897	4906	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	CDS	5692	5699	0.98	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	CDS	5987	6053	0.93	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	CDS	6827	6939	1	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig107816	AUGUSTUS	stop_codon	6937	6939	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [agtgtaagatggtgtgtatataccagtgtaagatggctgtgtattacagtttaagatggctgtgtatgtacagtgaaga
# ggctgtgtatatacagtgtaagatggctagtatgtacagtgtaagactggttgtgtatgacgtacagtgtgtaagatggctgttgtatgtagatgtaa
# gatggttgtgtatttgtagatatgtcccagaagaactactaccagtttataaggagaaaatattacctatagctgacatagtgactcccaatcagttt
# gaaacagaaatgttgacgggaatgaaaattaacagtgtggaggatgccattaaagcaatggaaattttacataacaaagggccaaaaaccgtggtcat
# cagcagcagtgagatcgcaacagatggcggcatcatcagcctggccagtaccgtcaccactcaccaaggccaaaggctcaagaaaacgtttaaacatc
# ttctccagaagcactgtaccagaagagtggagaataacatgagatgtcagacatgtagagtattatgtttcttctatccaacagatggccataaagaa
# gtatataaaatacagtttgaaaaggttccagccatatttgttggaactggggacttatttgccgcttgcctgcttgcatggttggagaaagacaaaaa
# cctgaagctccaggcagttgatcaagtggcatttgagaaaaccatatcaacacttcagtgtgtaatcaagcgaaccttagacagggccaaagttcttg
# ctggtgatggaaacacccccagtcccgctcagatggagctacgattagtgcagagtaaagcggatattgagaacccgccccatagctataccgcagct
# gtcttataa]
# protein sequence = [CKMVCIYQCKMAVYYSLRWLCMYSEEAVYIQCKMASMYSVRLVVYDVQCVRWLLYVDVRWLCICRYVPEELLPVYKEK
# ILPIADIVTPNQFETEMLTGMKINSVEDAIKAMEILHNKGPKTVVISSSEIATDGGIISLASTVTTHQGQRLKKTFKHLLQKHCTRRVENNMRCQTCR
# VLCFFYPTDGHKEVYKIQFEKVPAIFVGTGDLFAACLLAWLEKDKNLKLQAVDQVAFEKTISTLQCVIKRTLDRAKVLAGDGNTPSPAQMELRLVQSK
# ADIENPPHSYTAAVL]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370NIG.prfl --predictionStart=0  --predictionEnd=21900  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig10781620180911_busco_2432604931_.temp