# 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..11]--> unknown_A (14) <--[0..2]--> unknown_B (12) <--[3..4]--> unknown_C (15) <--[1..5]--> unknown_D (21) <--[3..13]--> unknown_E (21) <--[2..13]--> unknown_F (36) <--[0..22]--> unknown_G (50) <--[0..24]--> unknown_H (23) <--[0..1]--> unknown_I (9) <--[0..5]--> unknown_J (14) <--[2..15]--> unknown_K (28) <--[2..20]--> unknown_L (16) <--[0..1]--> unknown_M (19) <--[4..5]--> unknown_N (44) <--[2..6]--> unknown_O (17) <--[7..9]--> unknown_Q (13) <--[0..7]--> unknown_R (21) <--[0..5]--> unknown_S (25) <--[2..5]--> unknown_T (39) <--[0..1]--> unknown_U (19) <--[10..27]--> unknown_W (13) <--[0..5]--> unknown_X (27) <--[0..2]--> unknown_Y (37) <--[5..12]--> unknown_Z (30) <--[8..41]--> unknown_AB (41) <--[1..6]--> unknown_AC (12) <--[6..8]--> unknown_AE (20) <--[3..7]--> unknown_AF (17) <--[0..1]--> unknown_AG (14) <--[3..9]--> unknown_AH (34) <--[0..25]--> unknown_AI (23) <--[1..7]--> unknown_AJ (19) <--[12..35]--> unknown_AK (17) <--[10..15]--> unknown_AL (16) <--[18..38]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2038820180911_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 = 25695, name = Contig20388) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig20388	AUGUSTUS	gene	12848	16560	0.08	-	.	g1
Contig20388	AUGUSTUS	transcript	12848	16560	0.08	-	.	g1.t1
Contig20388	AUGUSTUS	stop_codon	12848	12850	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig20388	AUGUSTUS	intron	13005	13434	0.47	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig20388	AUGUSTUS	intron	13455	15569	0.52	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig20388	AUGUSTUS	intron	15667	16537	0.53	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig20388	AUGUSTUS	CDS	12848	13004	0.29	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig20388	AUGUSTUS	CDS	13435	13454	0.48	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig20388	AUGUSTUS	CDS	15570	15666	0.89	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig20388	AUGUSTUS	CDS	16538	16560	0.58	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig20388	AUGUSTUS	start_codon	16558	16560	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtttgcgtgggctctcaaaaggtgtaaactcctggcagctgttgtcagcctgtttgagctaccaaaggatgaatcaa
# ctccagatgatgaacattttattgaaattgaagacactcaggagattggggtaagtgggaggtgtaaactcctggcagctgttgtcagcctgtttgag
# ctaccaaaggatgaatcaactccagatgatgaacattttattgaaattgaagacactccaggtattcatgattattatcttgccaatgagcatcagat
# gattaactgtcgtgaagtttga]
# protein sequence = [MFAWALKRCKLLAAVVSLFELPKDESTPDDEHFIEIEDTQEIGVSGRCKLLAAVVSLFELPKDESTPDDEHFIEIEDT
# PGIHDYYLANEHQMINCREV]
# end gene g1
###
# start gene g2
Contig20388	AUGUSTUS	gene	26335	34074	0.11	-	.	g2
Contig20388	AUGUSTUS	transcript	26335	34074	0.11	-	.	g2.t1
Contig20388	AUGUSTUS	stop_codon	26335	26337	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	26435	26642	0.84	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	26725	27076	0.94	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	27163	28365	1	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	28464	28617	1	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	28821	30099	0.99	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	30251	30413	0.95	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	30512	30725	0.62	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	30830	31730	0.34	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	31871	32800	0.45	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	32863	33010	0.43	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	33096	33457	0.29	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	intron	33568	34074	0.83	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	26335	26434	0.82	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	26643	26724	0.94	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	27077	27162	0.94	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	28366	28463	1	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	28618	28820	1	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	30100	30250	0.96	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	30414	30511	0.62	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	30726	30829	0.42	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	31731	31870	0.54	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	32801	32862	0.46	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	33011	33095	0.4	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig20388	AUGUSTUS	CDS	33458	33567	0.83	-	2	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgtggacactagaagacgagctgcatgtgaccttgtccaggccctatgtaaatcgtttgagggtccggtcatccagaa
# cttttctcagtatgtccagggtctcctacagcatggtattacacaaaccagtacccttgtcaacattacagatttctaccaggcgcatattctccctg
# acattcagaattctgatgtcactgcaactcccattttaaaagcagatgccatcaaatacttaatgatatttaggaatcagctgcccgctgacgccttg
# gtagccagcgtccctaatctggtccagctcctgaaggtgcccagcatcgtcgtccattcttatgccgcccacaccgtagagagaatcttcatggttag
# aaagccagacggcagtggacctgttgttacacatgaacatattaagggttgtattggtgatctcatgaacagtctaataggggcaatgaaccacccag
# ggtcatcagagaacgaatacatcatgaaagctgtgatgagaagcatgtccacattgcaggagcatttgttacctctgatgggacaacttctgaaattc
# ctcacagaaaaactgggtcaagtcagcaagaatcccagcaagccacattttaatcactacctgtttgagtcgatgtgcgtggggatcagaacaacctg
# taaatacagtccggaggcagtggtccagtttgaacaagtcctgtttgaaccgttcacatttattctacagcaagatgtacaagagttcttaccatacg
# tctttcaaatcttgtctcttttgattgaccaccaccctaagggtaaagttgctgacacctatatggccctgtttccccacttaatggcccccgccttg
# tgggaaaggcctggaaatatccccccactggttcggcttctacaggcatacatagaaaaaggcgccaagcaaatagaggcagacaaaattaatggatt
# gttggggatattccagaaattgatagcttccaagactaatgatcatgaaggattttatcttttgaactccatcttggagcatatgcccagagagatca
# tagatgggtaccacaagcaaatctttatcctcttgttccagagattgtccagctctaaaacaaccaaatatatcaaaagtctgcttgtgttcttttca
# ttgtttgctacgattatcggagccagtcagttgctagatctgatcgatggaattcagccaagaagatctctggcgagtggagcagaagatctgtctgc
# gtgggtgaccaacatactgaccgaggctccagccatgctgcacaactacgaggctttctggtag]
# protein sequence = [VDTRRRAACDLVQALCKSFEGPVIQNFSQYVQGLLQHGITQTSTLVNITDFYQAHILPDIQNSDVTATPILKADAIKY
# LMIFRNQLPADALVASVPNLVQLLKVPSIVVHSYAAHTVERIFMVRKPDGSGPVVTHEHIKGCIGDLMNSLIGAMNHPGSSENEYIMKAVMRSMSTLQ
# EHLLPLMGQLLKFLTEKLGQVSKNPSKPHFNHYLFESMCVGIRTTCKYSPEAVVQFEQVLFEPFTFILQQDVQEFLPYVFQILSLLIDHHPKGKVADT
# YMALFPHLMAPALWERPGNIPPLVRLLQAYIEKGAKQIEADKINGLLGIFQKLIASKTNDHEGFYLLNSILEHMPREIIDGYHKQIFILLFQRLSSSK
# TTKYIKSLLVFFSLFATIIGASQLLDLIDGIQPRRSLASGAEDLSAWVTNILTEAPAMLHNYEAFW]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937050C.prfl --predictionStart=8380  --predictionEnd=53261  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2038820180911_busco_2432604931_.temp