# 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
# --[27..88]--> unknown_C (23) <--[16..27]--> unknown_E (14) <--[0..209]--> unknown_F (14) <--[0..3]--> unknown_G (24) <--[2..4]--> unknown_H (23) <--[2..3]--> unknown_I (24) <--[1..75]--> unknown_J (14) <--[0..1]--> unknown_K (14) <--[1..5]--> unknown_L (27) <--[8..224]--> unknown_M (23) <--[0..1]--> unknown_N (13) <--[0..70]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig7626620180911_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 = 3034, name = Contig76266) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig76266	AUGUSTUS	gene	1	2262	0.31	+	.	g1
Contig76266	AUGUSTUS	transcript	1	2262	0.31	+	.	g1.t1
Contig76266	AUGUSTUS	intron	1	304	0.81	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig76266	AUGUSTUS	intron	423	862	0.91	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig76266	AUGUSTUS	intron	931	1961	0.89	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig76266	AUGUSTUS	intron	2030	2128	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig76266	AUGUSTUS	CDS	305	422	0.82	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig76266	AUGUSTUS	CDS	863	930	0.91	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig76266	AUGUSTUS	CDS	1962	2029	1	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig76266	AUGUSTUS	CDS	2129	2262	0.43	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig76266	AUGUSTUS	stop_codon	2260	2262	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gtttataatgctctgtcaggcctccccagaagggattactgacaacatcattcagaaagggctgcctcagtgtgatacc
# aaacagaggatgaccatagtcaacaggcttctgtctatggggaagatagacctcttaaagagtggaaacaaactgttgtatcggctaaaagacccgga
# taccgcagcccaagtgaagggaggggacaatcaggagaagctggtgtatcagattatcaaagacgccggcaacaaaggaatctggataagggatatca
# gattcaagtgtaatctactgttaacgcaggtcaacaagattcttaaaaacctcgaaaccaaaaaattgattaaagctgtcaaatcagtcgctgtaagt
# atagaactcttgtaa]
# protein sequence = [FIMLCQASPEGITDNIIQKGLPQCDTKQRMTIVNRLLSMGKIDLLKSGNKLLYRLKDPDTAAQVKGGDNQEKLVYQII
# KDAGNKGIWIRDIRFKCNLLLTQVNKILKNLETKKLIKAVKSVAVSIELL]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370KOV.prfl --predictionStart=0  --predictionEnd=22458  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig7626620180911_busco_2432604931_.temp