# 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..34]--> unknown_A (18) <--[0..13]--> unknown_B (6) <--[0..9]--> unknown_C (30) <--[10..37]--> unknown_D (31) <--[0..2]--> unknown_E (9) <--[0..9]--> unknown_F (66) <--[0..3]--> unknown_G (33) <--[0..1]--> unknown_H (18) <--[6..45]--> unknown_J (24) <--[0..6]--> unknown_K (44) <--[0..8]--> unknown_L (55) <--[0..1]--> unknown_M (14) <--[0..23]--> unknown_N (58) <--[1..4]--> unknown_O (17) <--[2..5]--> unknown_P (35) <--[0..3]--> unknown_Q (120) <--[10..23]--> unknown_S (60) <--[2..11]--> unknown_T (41) <--[0..14]--> unknown_U (16) <--[0..2]--> unknown_V (41) <--[0..1]--> unknown_W (10) <--[0..1]--> unknown_X (25) <--[0..1]--> unknown_Y (27) <--[0..1]--> unknown_Z (22) <--[0..2]--> unknown_AA (14) <--[10..50]--> unknown_AC (10) <--[0..1]--> unknown_AD (40) <--[5..26]--> unknown_AE (19) <--[15..248]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4738720180911_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 = 8904, name = Contig47387) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig47387	AUGUSTUS	gene	4322	8356	0.36	-	.	g1
Contig47387	AUGUSTUS	transcript	4322	8356	0.36	-	.	g1.t1
Contig47387	AUGUSTUS	stop_codon	4322	4324	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig47387	AUGUSTUS	intron	4478	5253	0.53	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47387	AUGUSTUS	intron	5315	6427	0.85	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47387	AUGUSTUS	intron	6516	7362	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47387	AUGUSTUS	intron	7583	8284	0.8	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig47387	AUGUSTUS	CDS	4322	4477	0.77	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig47387	AUGUSTUS	CDS	5254	5314	0.85	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig47387	AUGUSTUS	CDS	6428	6515	0.93	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig47387	AUGUSTUS	CDS	7363	7582	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig47387	AUGUSTUS	CDS	8285	8356	0.81	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig47387	AUGUSTUS	start_codon	8354	8356	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtataaatcctcagtgaagcgcagcagtttattaattatcaatgagctacctgctgtaaagtttgcacaggagattg
# tgacacgccttggtcgatggatcgactttgagaacgactataagaccatgtaccccagctttatggagagcatctggtgggtgtttaaggagctctac
# agcaagggactagtgtataaagggtcaaaggtcatgcccttttccacggcctgtaacactccgctgtcaaacttcgagtcgggacagaattacaaaga
# cgtggtggatccagcagacaaatccacggggaaagtttacatcatgatggaggccaggctggaggctctgtttaagaaggaagacgaatacacaatcg
# tagagaaatttaagggaaggacgcttgaaggcaaaaaatatgagccagtatttccttacttcaaatatgatgattaccgagtatgtttgaagtacggt
# atcatcactcgagacatgaaaatcatctgccctgtggatgcgtctggaaagttcactgatcaggtcacagattttaagggacaatacgtcaaggtgat
# gtcactttcctcaattgagtacctttag]
# protein sequence = [MYKSSVKRSSLLIINELPAVKFAQEIVTRLGRWIDFENDYKTMYPSFMESIWWVFKELYSKGLVYKGSKVMPFSTACN
# TPLSNFESGQNYKDVVDPADKSTGKVYIMMEARLEALFKKEDEYTIVEKFKGRTLEGKKYEPVFPYFKYDDYRVCLKYGIITRDMKIICPVDASGKFT
# DQVTDFKGQYVKVMSLSSIEYL]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093701SQ.prfl --predictionStart=0  --predictionEnd=27585  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4738720180911_busco_2432604931_.temp