# 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
# --[3..109]--> unknown_A (14) <--[37..140]--> unknown_E (16) <--[0..89]--> unknown_F (27) <--[7..54]--> unknown_G (12) <--[0..8]--> unknown_H (14) <--[0..102]--> unknown_I (13) <--[1..8]--> unknown_J (13) <--[0..2]--> unknown_K (20) <--[3..41]--> unknown_L (12) <--[0..3]--> unknown_M (20) <--[0..1]--> unknown_N (6) <--[0..1]--> unknown_O (15) <--[0..3]--> unknown_P (21) <--[0..2]--> unknown_Q (77) <--[0..39]--> unknown_R (28) <--[0..5]--> unknown_S (12) <--[20..84]--> unknown_V (36) <--[1..33]--> unknown_W (21) <--[0..1]--> unknown_X (9) <--[0..5]--> unknown_Y (30) <--[7..51]--> unknown_Z (21) <--[0..1]--> unknown_AA (33) <--[0..6]--> unknown_AB (18) <--[0..8]--> unknown_AC (16) <--[2..20]--> unknown_AD (19) <--[1..58]--> unknown_AE (9) <--[0..4]--> unknown_AF (20) <--[1..7]--> unknown_AG (46) <--[0..41]--> unknown_AH (37) <--[24..71]--> unknown_AK (14) <--[51..153]--> unknown_AO (21) <--[18..748]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4300920180911_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 = 20371, name = Contig43009) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig43009	AUGUSTUS	gene	8512	20213	0.01	-	.	g1
Contig43009	AUGUSTUS	transcript	8512	20213	0.01	-	.	g1.t1
Contig43009	AUGUSTUS	stop_codon	8512	8514	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	intron	8592	10062	0.31	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	intron	10100	10553	0.16	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	intron	10779	10994	0.87	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	intron	11095	11516	0.77	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	intron	11631	11841	0.7	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	intron	11961	12502	0.71	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	intron	12637	15241	0.14	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	intron	15315	20135	0.35	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	CDS	8512	8591	0.68	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	CDS	10063	10099	0.28	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	CDS	10554	10778	0.56	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	CDS	10995	11094	1	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	CDS	11517	11630	0.7	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	CDS	11842	11960	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	CDS	12503	12636	0.35	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	CDS	15242	15314	0.42	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	CDS	20136	20213	0.38	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig43009	AUGUSTUS	start_codon	20211	20213	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaccattatcttcctcaggacaaagaagttgattacgtgtggaaaaactcaaaagtgcatgattacagaataccagg
# gttatgttgagcttctcatccatcctctgagacaggatctgaaaagagtgaagataaacagcaagcagtgtctgacagtcgacaatgatttgacagca
# gtgacctgtggtgacctcatcgaggtgatatccaccgccgacaaaaagcgaaagacgttccactatttcctgtcagttcccactgccgcacctaacat
# tggaatggctgcttttgagttctatgaggagctgctgtccagtagatacccgtactcttgctataaacatgtgtttgtggatgaagcttatgtagaat
# ccttgtcttatgccaccatgtctattttaagcacaaacctactacattccaacaggattatagatcagaccatcaccaccaggacagtcctagctgag
# gcagtggccaagcagttctttggaacattcattaccatgcaaacttggtctgatgcatggttaccaatggggatctcaggatatttaggtggcctctt
# catcaagaaaacttttggaaacaatgagtacagattcagaatttcaaatgactatgaaaacagagtgggaggaatcttactagatgccacaaagcggg
# actgcaatcatcacttctcaatcaaaaatccccacactgtgtccccacgctacatggaagccttcacctccaaatcactgttagtgatcagaatgtta
# gagcagaggattggtgaacagcttctgatacaggtcagtggtcaaatcaatagtcagaggtatcagtacctgatacaggtcagaggtcagtcagaggc
# accagtatctgatatagctatgagggatgttccgtgtacgtacaacaagataggagtcatattgacaagtcgtcaagcaagagaaaagcaacactaa]
# protein sequence = [MTIIFLRTKKLITCGKTQKCMITEYQGYVELLIHPLRQDLKRVKINSKQCLTVDNDLTAVTCGDLIEVISTADKKRKT
# FHYFLSVPTAAPNIGMAAFEFYEELLSSRYPYSCYKHVFVDEAYVESLSYATMSILSTNLLHSNRIIDQTITTRTVLAEAVAKQFFGTFITMQTWSDA
# WLPMGISGYLGGLFIKKTFGNNEYRFRISNDYENRVGGILLDATKRDCNHHFSIKNPHTVSPRYMEAFTSKSLLVIRMLEQRIGEQLLIQVSGQINSQ
# RYQYLIQVRGQSEAPVSDIAMRDVPCTYNKIGVILTSRQAREKQH]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093703W1.prfl --predictionStart=0  --predictionEnd=32745  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4300920180911_busco_2432604931_.temp