# 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..39]--> unknown_A (15) <--[0..2]--> unknown_B (26) <--[8..13]--> unknown_D (9) <--[3..6]--> unknown_E (24) <--[0..2]--> unknown_F (22) <--[1..22]--> unknown_G (29) <--[0..2]--> unknown_H (24) <--[0..1]--> unknown_I (23) <--[0..1]--> unknown_J (10) <--[4..12]--> unknown_K (32) <--[2..127]--> unknown_L (42) <--[10..43]--> unknown_M (15) <--[11..257]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig7617520180911_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 = 8047, name = Contig76175) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig76175	AUGUSTUS	gene	1103	7159	0.17	-	.	g1
Contig76175	AUGUSTUS	transcript	1103	7159	0.17	-	.	g1.t1
Contig76175	AUGUSTUS	stop_codon	1103	1105	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	intron	1854	2358	0.37	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	intron	2520	4277	0.49	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	intron	4351	5519	0.71	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	intron	5573	6480	0.74	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	intron	6599	6765	0.98	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	intron	6855	7135	0.96	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	CDS	1103	1853	0.37	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	CDS	2359	2519	0.49	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	CDS	4278	4350	1	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	CDS	5520	5572	0.87	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	CDS	6481	6598	0.75	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	CDS	6766	6854	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	CDS	7136	7159	0.93	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig76175	AUGUSTUS	start_codon	7157	7159	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaaggaatatgcttatatgaaggcgctgtatgacagaaagttcccagttcccaaaccagtggactttaacagacacg
# cagtagtaatggagcttatcagtggttaccctttgtgcaatgtgaagaatgtggctgacccagctcaaatgtaccatgactgtatggagctgatcgtg
# agattggggaactgtggggtgatccatggggattttaacgagtttaatttgatgttagctttcgacgacttgcaacagcagaaaatgccagtgtttat
# tttattaaaaagagatgatgatttggatgtggaagtatcagccagtggttttacaaaagaaatggcagaaacatttaatgagttctacaannnnnnnn
# nnnnnnnnnnnnnnnnnatcaaactgagcagtatatcagttgttgactggggctcagagggaaacagtcgatctgttggcaccggagtgcaagcctgt
# tccaaggctcgtatggccacgggcaacagctgcactccgtccaacaggaatattgtagaactgtttagtaaggggtataacaattacatttttgatgt
# ttcttctatgatcaagttattgttgcaggctgctgaggaatataacatcagaggaggacctgaaaatcccaaagcagcggactcagaagaggaggagt
# ccgatgaggattctgataatgcagatttagacgaggaggaacaagtgtcacaagagctgacaacgtctccagccgaggacagactaaatccctcagta
# agtgacttgtcagcaagcggtcacactgatcatagttcacaagggccgactacatctccagctgaggacagattaaatccttcagtaagtgacatgtc
# agcaagcggtcacactgataatcatccagaaagtggaaatgacagagtgacgggtgtagtcagtgcagaagaggaggacagtgtgagtggtagcgatg
# aggaagaccttgaggacctacatgatcaaaataggactttgagaccgttcagaaatgaggaaagcctcacacacaccaattcacacagaaggaaacat
# ctagacagtacaagtgtcagtgttaccagtaccacaagtagtatggaccccagacttgtcaaagagaaagtaaaacaacagatgaaaaagaaagcggc
# agtaaaggaagctaggaggatacgaaagagtggagagtctgcaatgattaccaagaaaaagagggacatttctcaagatatcaagcaaagtgtggatg
# ctggctggtattaa]
# protein sequence = [MKEYAYMKALYDRKFPVPKPVDFNRHAVVMELISGYPLCNVKNVADPAQMYHDCMELIVRLGNCGVIHGDFNEFNLML
# AFDDLQQQKMPVFILLKRDDDLDVEVSASGFTKEMAETFNEFYXXXXXXXXXIKLSSISVVDWGSEGNSRSVGTGVQACSKARMATGNSCTPSNRNIV
# ELFSKGYNNYIFDVSSMIKLLLQAAEEYNIRGGPENPKAADSEEEESDEDSDNADLDEEEQVSQELTTSPAEDRLNPSVSDLSASGHTDHSSQGPTTS
# PAEDRLNPSVSDMSASGHTDNHPESGNDRVTGVVSAEEEDSVSGSDEEDLEDLHDQNRTLRPFRNEESLTHTNSHRRKHLDSTSVSVTSTTSSMDPRL
# VKEKVKQQMKKKAAVKEARRIRKSGESAMITKKKRDISQDIKQSVDAGWY]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370E4U.prfl --predictionStart=0  --predictionEnd=27258  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig7617520180911_busco_2432604931_.temp