# 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
# --[4..231]--> unknown_A (20) <--[0..3]--> unknown_B (24) <--[34..68]--> unknown_E (43) <--[0..11]--> unknown_F (24) <--[10..76]--> unknown_H (17) <--[2..37]--> unknown_I (17) <--[15..22]--> unknown_J (17) <--[19..84]--> unknown_M (22) <--[8..30]--> unknown_N (44) <--[1..6]--> unknown_O (10) <--[0..2]--> unknown_P (20) <--[41..126]--> unknown_T (10) <--[5..11]--> unknown_U (30) <--[2..11]--> unknown_V (18) <--[17..43]--> unknown_W (22) <--[0..4]--> unknown_X (27) <--[0..48]--> unknown_Y (27) <--[11..30]--> unknown_Z (25) <--[6..50]--> unknown_AA (46) <--[1..3]--> unknown_AB (17) <--[3..26]--> unknown_AC (22) <--[0..1]--> unknown_AD (11) <--[14..54]--> unknown_AE (14) <--[7..26]--> unknown_AG (18) <--[0..49]--> unknown_AH (14) <--[0..1]--> unknown_AI (17) <--[8..111]--> unknown_AJ (17) <--[11..80]--> unknown_AL (11) <--[7..44]--> unknown_AM (18) <--[0..601]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3938920180911_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 = 8648, name = Contig39389) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig39389	AUGUSTUS	gene	1	8130	0.04	-	.	g1
Contig39389	AUGUSTUS	transcript	1	8130	0.04	-	.	g1.t1
Contig39389	AUGUSTUS	intron	1	439	0.63	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	intron	604	1530	0.46	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	intron	1693	2217	0.48	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	intron	2359	5938	0.63	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	intron	6126	6265	0.52	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	intron	6383	6561	0.58	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	intron	6844	8118	0.83	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	CDS	440	603	0.61	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	CDS	1531	1692	0.47	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	CDS	2218	2358	0.72	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	CDS	5939	6125	0.5	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	CDS	6266	6382	0.57	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	CDS	6562	6843	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	CDS	8119	8130	0.83	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig39389	AUGUSTUS	start_codon	8128	8130	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgattagacatatttcaaagaaacgcaacaccaacactagctctgttgatgatgaagagaggaatgggtcaccagcac
# tcagggaaaatgactctgaagagtcggacacaaatgacagtgagaccgagagcatggacaatgacccccagacagaggctgagtcatcagatgaaccg
# ccggggaaaaaagcaaaaatgtccaagaaggatctctacagaccccccactaacgaggagctgaaccaactgaaggaaacccagaacctgtttcactc
# aagtctgttccgattgcaggtgaatgaactactgaaggaggttcaggtcaaggccaagcgacagagacagatagaggatgcagtggaaacggtcacgc
# aaatgatcaaatctctcaagaaaagtgtagaacatgagctgcagtcacagaaatggctgaagaaagtccgagtccctatccaccagagacccccagca
# gtgaagggcaggttccagtttgtaccccccacggagatactgaccactggcagtgttgtgacagggacgtgcatcaaacctcacgttacagtggacgt
# cgtgctggtcattccaaaggtacggaaagatggtgagcacaaaccagtctgcctgagcctcagcgctgtaccggaggagggtgtgtttaagatgaacc
# gatttcacatcaacaagaataacgttcgacggcagtggttcatggaggaaggggcgggcgactctgacacagataagacatgccctactccattttat
# aacaactcggtcttacatctagcatggtccaggaaaacacaagcttcctcgcgaggagaaccctggggagattctcagagcatcaagacggcattgct
# cttcagtcaagtctggctcgacaaagggactcactattcccagacagattggaccaaggagccgttaaccctctgttcgacctttgacccttacaacc
# agcctgacccttgcgtattttacgaacacttcagtgttgtgtttgtggatgtgactggtcatgttaatttgtgttctgatgtcagtaaaggcctctac
# gacagg]
# protein sequence = [MIRHISKKRNTNTSSVDDEERNGSPALRENDSEESDTNDSETESMDNDPQTEAESSDEPPGKKAKMSKKDLYRPPTNE
# ELNQLKETQNLFHSSLFRLQVNELLKEVQVKAKRQRQIEDAVETVTQMIKSLKKSVEHELQSQKWLKKVRVPIHQRPPAVKGRFQFVPPTEILTTGSV
# VTGTCIKPHVTVDVVLVIPKVRKDGEHKPVCLSLSAVPEEGVFKMNRFHINKNNVRRQWFMEEGAGDSDTDKTCPTPFYNNSVLHLAWSRKTQASSRG
# EPWGDSQSIKTALLFSQVWLDKGTHYSQTDWTKEPLTLCSTFDPYNQPDPCVFYEHFSVVFVDVTGHVNLCSDVSKGLYDR]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093702PE.prfl --predictionStart=0  --predictionEnd=23099  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3938920180911_busco_2432604931_.temp