# 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
# --[17..310]--> unknown_A (14) <--[1..5]--> unknown_B (19) <--[4..8]--> unknown_C (14) <--[2..5]--> unknown_D (10) <--[0..2]--> unknown_E (14) <--[0..18]--> unknown_F (32) <--[0..1]--> unknown_G (31) <--[1..2]--> unknown_H (24) <--[10..28]--> unknown_J (23) <--[0..1]--> unknown_K (20) <--[13..64]--> unknown_L (72) <--[8..21]--> unknown_N (16) <--[14..83]--> unknown_P (18) <--[51..202]--> unknown_S (16) <--[18..49]--> unknown_V (12) <--[0..89]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig8738620180911_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 = 10101, name = Contig87386) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig87386	AUGUSTUS	gene	329	8741	0.02	-	.	g1
Contig87386	AUGUSTUS	transcript	329	8741	0.02	-	.	g1.t1
Contig87386	AUGUSTUS	stop_codon	329	331	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	intron	480	2334	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	intron	2448	2633	0.47	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	intron	2899	3369	0.69	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	intron	3517	5371	0.92	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	intron	5485	5598	0.31	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	intron	5659	7534	0.6	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	intron	7670	7760	0.83	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	intron	7790	8447	0.81	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	intron	8534	8691	0.39	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	CDS	329	479	0.6	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	CDS	2335	2447	0.47	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	CDS	2634	2898	0.72	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	CDS	3370	3516	0.93	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	CDS	5372	5484	0.47	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	CDS	5599	5658	0.47	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	CDS	7535	7669	0.88	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	CDS	7761	7789	0.81	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	CDS	8448	8533	0.81	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	CDS	8692	8741	0.4	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig87386	AUGUSTUS	start_codon	8739	8741	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcacacagcgccagcttcgctgatttatttgccagatccagcgatcatgaattctcacaacgaggcatatggttcct
# gcatttgtttcatggtcgtcagaacgcaattaacagattatgaggatctgtatgcgtgacttccaaatcacttcgacataaccatggacaggaaagtg
# ataatgaagacctttaagacacacgtgactaagatctgtaaagacgaatacggatatctggtcctgattgcgctgtttgatgtggtggacgatacaaa
# actagtgggcaagatcataatcgaggagggcgacaacaacccccacagtaatacagtgttaggaggcgacaacaacccccaccaggtaaacagtgtag
# gagggcgagcaacaccccctctatcagggaataacggtgtagaggcgacaacaccccacagtaattacggtgtaggagccatgactaacaaccccaac
# agtagaaggattcagcggtacgatacctggagtttattgacgctgtggtgtcccctcctctactacagttacatcgtggagcacgctcgagaccgttt
# atggagaacggctcgttactgctgttctgtcaaattcttaactacgcttcgattgaatttacaggaaatgttaaagtccttgtcagagattgctcaga
# gtcaacatggaaggaaggttttccagtacatcctgtgccccagggacccccatttcttccagccagacgttgtccgcgtccttaaggagggcgacaac
# aaccctcacagtaaatacggtgtaggagggcgacaaacaacccccacaggtaatacagttagaggcgacaacaaccccagcaggaatacagtgttagg
# aggcgacaacaaccccccacaggtaaacagtgtaggagggcgagcaacaccccctctatcagggaataacggtgtagaggcgacaacaccccacagta
# attacggtgtaggagccatgactaacaaccccaacagtagaaggattcagcggtacgatacctggagtttattgacgctgtggtgtcccctcctctac
# tacagttacatcgtggagcacgctcgagaccgtttatggagaacggctcgttactgctgttctgtcaaattcttaactacgcttcggtaa]
# protein sequence = [MHTAPASLIYLPDPAIMNSHNEAYGSCICFMVVRTQLTDYEDLYAXLPNHFDITMDRKVIMKTFKTHVTKICKDEYGY
# LVLIALFDVVDDTKLVGKIIIEEGDNNPHSNTVLGGDNNPHQVNSVGGRATPPLSGNNGVEATTPHSNYGVGAMTNNPNSRRIQRYDTWSLLTLWCPL
# LYYSYIVEHARDRLWRTARYCCSVKFLTTLRLNLQEMLKSLSEIAQSQHGRKVFQYILCPRDPHFFQPDVVRVLKEGDNNPHSKYGVGGRQTTPTGNT
# VRGDNNPSRNTVLGGDNNPPQVNSVGGRATPPLSGNNGVEATTPHSNYGVGAMTNNPNSRRIQRYDTWSLLTLWCPLLYYSYIVEHARDRLWRTARYC
# CSVKFLTTLR]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370DTG.prfl --predictionStart=0  --predictionEnd=27678  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig8738620180911_busco_2432604931_.temp