# 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..35]--> unknown_A (14) <--[0..1]--> unknown_B (67) <--[8..30]--> unknown_C (18) <--[0..18]--> unknown_D (22) <--[2..32]--> unknown_E (30) <--[1..6]--> unknown_F (12) <--[8..20]--> unknown_H (27) <--[0..1]--> unknown_I (12) <--[2..5]--> unknown_J (11) <--[0..32]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig20241720180911_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 = 3122, name = Contig202417) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig202417	AUGUSTUS	gene	1	2182	0.08	-	.	g1
Contig202417	AUGUSTUS	transcript	1	2182	0.08	-	.	g1.t1
Contig202417	AUGUSTUS	intron	1	1034	0.42	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig202417	AUGUSTUS	intron	1179	1649	0.86	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig202417	AUGUSTUS	intron	1784	2146	0.36	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig202417	AUGUSTUS	CDS	1035	1178	0.91	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig202417	AUGUSTUS	CDS	1650	1783	0.79	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig202417	AUGUSTUS	CDS	2147	2182	0.28	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig202417	AUGUSTUS	start_codon	2180	2182	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgctgggggtgggggacttctactacgaactcggcgggtttggtctctttgctgacaaaccttcaatggtttttcaga
# ctgacttatattttacaggtctgatcggtatagaggagctgagagataaagtgatggcatctaggggaaagaagagtcaagccatttctctagatgat
# ttattacgtgcaataaagaagctgaaagttcttgggaatggtttcactctgatttccctgggaaagagctacatggtacagagcgtaccaggggagtt
# aactatggatcataccaaactgcttacaggaaggctcag]
# protein sequence = [MLGVGDFYYELGGFGLFADKPSMVFQTDLYFTGLIGIEELRDKVMASRGKKSQAISLDDLLRAIKKLKVLGNGFTLIS
# LGKSYMVQSVPGELTMDHTKLLTGRL]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370O06.prfl --predictionStart=0  --predictionEnd=22212  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig20241720180911_busco_2432604931_.temp