# 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..48]--> unknown_A (28) <--[1..13]--> unknown_B (9) <--[0..2]--> unknown_C (18) <--[8..33]--> unknown_D (24) <--[6..13]--> unknown_F (10) <--[0..21]--> unknown_G (13) <--[1..2]--> unknown_H (65) <--[9..47]--> unknown_J (67) <--[3..8]--> unknown_K (18) <--[0..1]--> unknown_L (22) <--[0..19]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4152920180911_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 = 11459, name = Contig41529) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig41529	AUGUSTUS	gene	389	3018	0.26	-	.	g1
Contig41529	AUGUSTUS	transcript	389	3018	0.26	-	.	g1.t1
Contig41529	AUGUSTUS	stop_codon	389	391	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig41529	AUGUSTUS	intron	1382	2982	0.26	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig41529	AUGUSTUS	CDS	389	1381	0.35	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig41529	AUGUSTUS	CDS	2983	3018	0.36	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig41529	AUGUSTUS	start_codon	3016	3018	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcttactcatcctaggcacctgatcccacctctgggaaaagagaaaataaatacgtcaaatttctactggaagttga
# ggaattcattaccagacagattcgcctgtttgaaccttttatcatctgacagatattttgaagtggaatgtcctccaactaccttaaatgatcagcaa
# atgattgctatagaaaaggttaaacagtgcgttgttgagaccgttacgcatatgcctcattggggggaagaaatcccttcaaactggataaagtttgt
# cggtattctcaataaaaagaaagaagaaggagttagaatcctgagaagagataccctgcgtatatttgaagaactaggattttcaactgatgaggatt
# tgaatgacatgcttcgatttttccagcagattggatacataatttattttgcagatgagggattgagggacacaattataatcaatgtccaatggttt
# gttgacgcctttaaatacatcatcaccgatcgaaaacacataccacccgaaaatactgtatgtgacaaatggatgcaaacgggaagaattccagaatc
# ggcctttcataaaatctggagagattccaatgacatttggtactttgtgcatcaaaatgacattctaccatacatgcagaaacttggactaattaccc
# agaaactggaggactcagaaactaatggaagcatgtactacgtcccgagcatgaacagagtagacttttctccaaaatttctagatgtaatcaacaga
# ggtcacaaaacatctattctcgttttccatttcaagacgtatatgccgcattttttcttctttcgtctgggttgtacattgttcagcaaagtgggaag
# agctcaatccaacaaatgttttgtaaaaatgcagcatttacaaggacacaggattatagccattgcattgccattgctgtcaacacaacatcgattct
# gtgcaagtattacactggacaagaacacaaatctacagacggagaattgttgtgggaataaagagtga]
# protein sequence = [MLTHPRHLIPPLGKEKINTSNFYWKLRNSLPDRFACLNLLSSDRYFEVECPPTTLNDQQMIAIEKVKQCVVETVTHMP
# HWGEEIPSNWIKFVGILNKKKEEGVRILRRDTLRIFEELGFSTDEDLNDMLRFFQQIGYIIYFADEGLRDTIIINVQWFVDAFKYIITDRKHIPPENT
# VCDKWMQTGRIPESAFHKIWRDSNDIWYFVHQNDILPYMQKLGLITQKLEDSETNGSMYYVPSMNRVDFSPKFLDVINRGHKTSILVFHFKTYMPHFF
# FFRLGCTLFSKVGRAQSNKCFVKMQHLQGHRIIAIALPLLSTQHRFCASITLDKNTNLQTENCCGNKE]
# end gene g1
###
# start gene g2
Contig41529	AUGUSTUS	gene	5841	6378	0.37	-	.	g2
Contig41529	AUGUSTUS	transcript	5841	6378	0.37	-	.	g2.t1
Contig41529	AUGUSTUS	stop_codon	5841	5843	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig41529	AUGUSTUS	intron	5932	6160	0.63	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig41529	AUGUSTUS	CDS	5841	5931	0.61	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig41529	AUGUSTUS	CDS	6161	6378	0.59	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig41529	AUGUSTUS	start_codon	6376	6378	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgatggcccgagtccttgattatggtgaaccttccaaagcctttctggtgacaaacggagtcaaacaaggatgtgtcc
# tagccccaacactcttcaacatgatgttttcagaaatgctgtctgacgccttcagaggtaatgatcctggcatcaacatcaaattcaggacagatgga
# aagctgtttgacctctcagacatctgcaggctgtctcgaaacagcaccctctcccgcaatgtcaacatcgctgccgaaatcaacaacagaatcacaaa
# ggcaagcagcgcctttggtagactgcggatttaa]
# protein sequence = [MMARVLDYGEPSKAFLVTNGVKQGCVLAPTLFNMMFSEMLSDAFRGNDPGINIKFRTDGKLFDLSDICRLSRNSTLSR
# NVNIAAEINNRITKASSAFGRLRI]
# end gene g2
###
# start gene g3
Contig41529	AUGUSTUS	gene	8693	11284	0.32	-	.	g3
Contig41529	AUGUSTUS	transcript	8693	11284	0.32	-	.	g3.t1
Contig41529	AUGUSTUS	stop_codon	8693	8695	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig41529	AUGUSTUS	intron	8915	9035	0.95	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig41529	AUGUSTUS	intron	9172	9457	0.97	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig41529	AUGUSTUS	intron	9714	10294	0.99	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig41529	AUGUSTUS	intron	10463	11262	0.76	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig41529	AUGUSTUS	CDS	8693	8914	0.9	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig41529	AUGUSTUS	CDS	9036	9171	0.92	-	1	transcript_id "g3.t1"; gene_id "g3";
Contig41529	AUGUSTUS	CDS	9458	9713	0.97	-	2	transcript_id "g3.t1"; gene_id "g3";
Contig41529	AUGUSTUS	CDS	10295	10462	0.77	-	2	transcript_id "g3.t1"; gene_id "g3";
Contig41529	AUGUSTUS	CDS	11263	11284	0.44	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig41529	AUGUSTUS	start_codon	11282	11284	.	-	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgagaagaagactttgcgaagttcagtatcagatggaaatgatgagaaacttgagacatgtaaacatagaccatcttc
# atgtaggctggtaccaaagtaccttgtttggttccttcatcagcagagctttcctagattctcagtttaactaccaacactccattgaggagtctgtg
# gtgctcatctatgatccacttcgttcaacacaaggattccttgctttgaaagcttaccgcctgaaacccgagatgatggacttctacagagaagggga
# cttcaccccagaagccatacaagcagccaacattagtttcgagtcaatgtttgaagagatcccagtgacaattaagaactcacacctggtcaatgctc
# tattgtgtgagatagaggagagtcctaaatctcgggaggaggagacttgtaacttcatggatttagctacaagctccatgttagagaaaaacttgcga
# caattaatgggctgtgttgatgaggtagctatggacgccaacagatttctgaactatcaaaggcagtatcagaaacaaatcattcagaaacagcagta
# tctacagaaaaggcaacaagaaaaccagcagagaatatctaaaggagataccccactaccagatgaagatatcaacaaggtcttcaagcctattccca
# cacctgcccggctggacagtctgctattggcaggacaaattgacaattactgtcaccagattcaggagtttgcctcccagagctttgggaaacttttt
# atggccgacagtctgcagagtgaaacgaaagaaagttaa]
# protein sequence = [MRRRLCEVQYQMEMMRNLRHVNIDHLHVGWYQSTLFGSFISRAFLDSQFNYQHSIEESVVLIYDPLRSTQGFLALKAY
# RLKPEMMDFYREGDFTPEAIQAANISFESMFEEIPVTIKNSHLVNALLCEIEESPKSREEETCNFMDLATSSMLEKNLRQLMGCVDEVAMDANRFLNY
# QRQYQKQIIQKQQYLQKRQQENQQRISKGDTPLPDEDINKVFKPIPTPARLDSLLLAGQIDNYCHQIQEFASQSFGKLFMADSLQSETKES]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370VFL.prfl --predictionStart=0  --predictionEnd=30448  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4152920180911_busco_2432604931_.temp