# 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..66]--> unknown_A (18) <--[2..5]--> unknown_B (35) <--[0..1]--> unknown_C (13) <--[17..66]--> unknown_F (22) <--[0..4]--> unknown_G (11) <--[0..8]--> unknown_H (14) <--[0..138]--> unknown_I (17) <--[0..2]--> unknown_J (56) <--[0..3]--> unknown_K (16) <--[10..63]--> unknown_L (9) <--[1..2]--> unknown_M (6) <--[0..5]--> unknown_N (47) <--[14..144]--> unknown_P (31) <--[16..51]--> unknown_R (33) <--[0..29]--> unknown_S (33) <--[1..9]--> unknown_T (32) <--[14..118]--> unknown_V (25) <--[13..97]--> unknown_X (39) <--[27..186]--> unknown_Z (17) <--[32..604]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5255620180911_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 = 5582, name = Contig52556) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig52556	AUGUSTUS	gene	155	3176	0.22	-	.	g1
Contig52556	AUGUSTUS	transcript	155	3176	0.22	-	.	g1.t1
Contig52556	AUGUSTUS	stop_codon	155	157	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig52556	AUGUSTUS	intron	296	629	0.92	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig52556	AUGUSTUS	intron	776	1075	0.88	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig52556	AUGUSTUS	intron	1125	1580	0.75	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig52556	AUGUSTUS	intron	1610	3136	0.57	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig52556	AUGUSTUS	CDS	155	295	0.91	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig52556	AUGUSTUS	CDS	630	775	0.93	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig52556	AUGUSTUS	CDS	1076	1124	0.78	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig52556	AUGUSTUS	CDS	1581	1609	0.74	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig52556	AUGUSTUS	CDS	3137	3176	0.31	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig52556	AUGUSTUS	start_codon	3174	3176	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtctctactctatgaatgcatcaataccgtaatagcaggcatccccaatcataccgcctcaattcagctctgtgtcc
# agaagttaaggattttgattgaagattctgatcagaacttgaagtatcttggtctgctggcaatgtccaaaattctggccacacatcccaagagtgtc
# cagtcacataaagatctgattcttcagtgtttggatgataaagacgagtccatcagactgagggccctggacctgatttacggaatgaacttgatgga
# gatcgtgaagaagttaatggtgcacatggataaggcggagggcacccactacagggacgaactgctggccaagatcgtggagatctccagccagtcaa
# actaccagtacatcacaaactttgaatggtag]
# protein sequence = [MSLLYECINTVIAGIPNHTASIQLCVQKLRILIEDSDQNLKYLGLLAMSKILATHPKSVQSHKDLILQCLDDKDESIR
# LRALDLIYGMNLMEIVKKLMVHMDKAEGTHYRDELLAKIVEISSQSNYQYITNFEW]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG0937033T.prfl --predictionStart=0  --predictionEnd=24676  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5255620180911_busco_2432604931_.temp