# 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
# --[2..124]--> unknown_A (10) <--[0..6]--> unknown_B (16) <--[0..4]--> unknown_C (22) <--[0..4]--> unknown_D (19) <--[0..13]--> unknown_E (41) <--[0..34]--> unknown_F (22) <--[0..1]--> unknown_G (9) <--[7..9]--> unknown_I (20) <--[12..54]--> unknown_K (27) <--[4..13]--> unknown_L (28) <--[3..8]--> unknown_M (60) <--[0..1]--> unknown_N (91) <--[9..30]--> unknown_P (16) <--[14..100]--> unknown_Q (12) <--[12..175]--> unknown_R (38) <--[20..65]--> unknown_T (19) <--[9..17]--> unknown_U (21) <--[6..43]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig21298620180911_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 = 5899, name = Contig212986) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig212986	AUGUSTUS	gene	1	4605	0.53	+	.	g1
Contig212986	AUGUSTUS	transcript	1	4605	0.53	+	.	g1.t1
Contig212986	AUGUSTUS	intron	1	1439	0.72	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig212986	AUGUSTUS	intron	1582	2664	0.65	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig212986	AUGUSTUS	intron	2742	3093	0.77	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig212986	AUGUSTUS	intron	3192	3424	0.98	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig212986	AUGUSTUS	intron	3502	4443	1	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig212986	AUGUSTUS	CDS	1440	1581	0.68	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig212986	AUGUSTUS	CDS	2665	2741	0.77	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig212986	AUGUSTUS	CDS	3094	3191	0.92	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig212986	AUGUSTUS	CDS	3425	3501	0.99	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig212986	AUGUSTUS	CDS	4444	4605	1	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig212986	AUGUSTUS	stop_codon	4603	4605	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gagcttccgggggcttcgcccctggaccccaccagggtttgccctggacccacttggggcctttaaggcggcccagacc
# cctgcctctgaaaaaaaaatccagccccccctaaccaaaattcctggatccgcccctggaatggttatggagggtgttttgaaaacaattgcaaacaa
# cttcatcacagacaggaatgcaggagaagtgatggcagtggggctgaatgcagtgaaggagatttgtactcgatgtcccttggccatgactcaagatt
# tgctgggtgatttgctgcagtacaaatcacatagagataaaggtgtcatgatgggtgccagagccctactgcagctgtacaggagagtaaatcctgaa
# ctcctgaacaagaaagccaagggtcgaccaacagaagctatggcagaggcagaaccattggtgtatggaggtcatactgccaaggattttatctcggg
# ggcggaaattctaccagaggaggaagaacagaaggagacagaagaaaatggtatacagagtgagatagatacaacacagagttga]
# protein sequence = [SFRGLRPWTPPGFALDPLGAFKAAQTPASEKKIQPPLTKIPGSAPGMVMEGVLKTIANNFITDRNAGEVMAVGLNAVK
# EICTRCPLAMTQDLLGDLLQYKSHRDKGVMMGARALLQLYRRVNPELLNKKAKGRPTEAMAEAEPLVYGGHTAKDFISGAEILPEEEEQKETEENGIQ
# SEIDTTQS]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093707HK.prfl --predictionStart=0  --predictionEnd=23193  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig21298620180911_busco_2432604931_.temp