# 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..42]--> unknown_A (20) <--[0..1]--> unknown_B (51) <--[1..2]--> unknown_C (21) <--[1..18]--> unknown_D (14) <--[0..2]--> unknown_E (12) <--[0..1]--> unknown_F (26) <--[0..15]--> unknown_G (27) <--[0..1]--> unknown_H (16) <--[0..33]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2920020180911_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 = 7793, name = Contig29200) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig29200	AUGUSTUS	gene	1	6918	0.16	-	.	g1
Contig29200	AUGUSTUS	transcript	1	6918	0.16	-	.	g1.t1
Contig29200	AUGUSTUS	intron	1	67	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	intron	118	707	0.96	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	intron	871	1387	0.88	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	intron	1459	2095	0.66	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	intron	2219	2668	0.52	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	intron	2766	6864	0.29	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	CDS	68	117	0.95	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	CDS	708	870	0.97	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	CDS	1388	1458	0.84	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	CDS	2096	2218	0.47	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	CDS	2669	2765	0.76	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	CDS	6865	6918	0.53	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig29200	AUGUSTUS	start_codon	6916	6918	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtgtcttactttgggactgacccgagtagaaccagtgtcagccgtaacaaaatggagcatagggctgcaactacgcc
# tcgccacgaactctgttctgggctgctttcttcagctggatccatgtcatcccagtgttctttacttcgcagacaccgacaaaatgcacagaatgaca
# gataatctcgtgatgctggttagtggagaatcaggagacactgtacagtttgcggaattcatttctaagaatattcaactctacaagatgagaaatgg
# atatgatttatcaccaacagctgcagccaacttcacacggaaaaatttggcggactatcttagaagtcggacaccatacatggtgaatctcctcatgg
# ccggattcgacaaaaatgagggaccatctctctactttatggactacttagcctcaatgaacaaatgtccttttgctgcccatggttatggagccttt
# ttctccctcgctatattggacagatactacacagaagacttgacaagagcaagagcaatagagctactaaccatgtgtatagaggag]
# protein sequence = [MCLTLGLTRVEPVSAVTKWSIGLQLRLATNSVLGCFLQLDPCHPSVLYFADTDKMHRMTDNLVMLVSGESGDTVQFAE
# FISKNIQLYKMRNGYDLSPTAAANFTRKNLADYLRSRTPYMVNLLMAGFDKNEGPSLYFMDYLASMNKCPFAAHGYGAFFSLAILDRYYTEDLTRARA
# IELLTMCIEE]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370TG6.prfl --predictionStart=0  --predictionEnd=22225  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2920020180911_busco_2432604931_.temp