# 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..1348]--> unknown_A (28) <--[0..1]--> unknown_B (22) <--[0..29]--> unknown_C (35) <--[6..23]--> unknown_E (27) <--[0..128]--> unknown_F (37) <--[0..200]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig540520180911_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 = 17382, name = Contig5405) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig5405	AUGUSTUS	gene	1	15579	0.01	-	.	g1
Contig5405	AUGUSTUS	transcript	1	15579	0.01	-	.	g1.t1
Contig5405	AUGUSTUS	intron	1	1393	0.7	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	intron	1540	2477	0.76	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	intron	2587	2942	0.39	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	intron	3045	8949	0.08	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	intron	9033	10759	0.15	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	intron	10861	11532	0.15	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	intron	11563	11681	0.43	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	intron	11885	12779	0.74	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	intron	12847	15131	0.58	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	intron	15235	15504	0.82	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	CDS	1394	1539	0.75	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	CDS	2478	2586	0.83	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	CDS	2943	3044	0.18	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	CDS	8950	9032	0.11	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	CDS	10760	10860	0.21	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	CDS	11533	11562	0.45	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	CDS	11682	11884	0.45	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	CDS	12780	12846	0.75	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	CDS	15132	15234	0.66	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	CDS	15505	15579	0.41	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig5405	AUGUSTUS	start_codon	15577	15579	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtccnattgtgatgcctgtagggagagctctgctttggccagcaagagggctttgctggggctgcctctattgacta
# gagattttttggagtggttgggtcttggtctgttggtccatttcattttctccctttcatttacatttgattccatagagcagaccctggaactgaca
# gatcctgatcccatctgggaagaagagacttctgatatgttaaagtcctggcaaacggcacaaggaagtttacaggaacgcctcatgacggggacatt
# tatcgaagcctttgaaaaactcagtaggatgacatccgttggcggctttgccctccttcaagtcgatagtacgaagtcaggtctggatggtgagaatc
# agctgactctcacagccgagcgtctctttcggaaactgtggctgggcatcatgagtatgttggttggctctccaggtgccgacattcaccgcttccac
# tctgctgatttctcaactaagctacatgaaccaaagtcttaccataaacttggtgaaatagtgctgcactctgcattcattgcgcttaaatctgccct
# atttccagagtgctgcgacccgagtttgatccttgtgatcgcctcgatctctcctttaagcttcgagaggtatcaaattggttctctagcagtcacca
# tggctacaaaagttactgccaatccagaaatagatattttgaaagaagaacgagaaggaagacttcgtgaagttggaaatcaggctgtgtggtcgttg
# ttgtgtgcctttgaggatgaagacattttaaggagggaggagtgtagtggtcagctgggtttgatctctggtggcctgatagctcagttggtagagca
# cctgattggactcctggacaatacagtggacacatactggcagtcagatggaccccaacctcacctggtcaacatccaattcagacgaaagaccacca
# tccatgacgtctgcatatacacagattacaaagcagacgagagctacacaccaaatag]
# protein sequence = [MSXCDACRESSALASKRALLGLPLLTRDFLEWLGLGLLVHFIFSLSFTFDSIEQTLELTDPDPIWEEETSDMLKSWQT
# AQGSLQERLMTGTFIEAFEKLSRMTSVGGFALLQVDSTKSGLDGENQLTLTAERLFRKLWLGIMSMLVGSPGADIHRFHSADFSTKLHEPKSYHKLGE
# IVLHSAFIALKSALFPECCDPSLILVIASISPLSFERYQIGSLAVTMATKVTANPEIDILKEEREGRLREVGNQAVWSLLCAFEDEDILRREECSGQL
# GLISGGLIAQLVEHLIGLLDNTVDTYWQSDGPQPHLVNIQFRRKTTIHDVCIYTDYKADESYTPN]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370S4T.prfl --predictionStart=0  --predictionEnd=30318  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig540520180911_busco_2432604931_.temp