# 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
# --[9..505]--> unknown_B (38) <--[4..24]--> unknown_C (67) <--[0..1]--> unknown_D (6) <--[0..1]--> unknown_E (24) <--[1..9]--> unknown_F (67) <--[6..108]--> unknown_G (31) <--[4..7]--> unknown_H (38) <--[1..5]--> unknown_I (16) <--[0..1]--> unknown_J (56) <--[8..14]--> unknown_K (58) <--[0..297]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3894020180911_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 = 24665, name = Contig38940) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig38940	AUGUSTUS	gene	5031	5369	0.43	+	.	g1
Contig38940	AUGUSTUS	transcript	5031	5369	0.43	+	.	g1.t1
Contig38940	AUGUSTUS	start_codon	5031	5033	.	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig38940	AUGUSTUS	CDS	5031	5369	0.43	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig38940	AUGUSTUS	stop_codon	5367	5369	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgcttaccttcttatgcgcctgcgttttccagagggagcggactgtcccgatgactagactcgcaatggaattactat
# ctatctatctttctccggctgacttttcgtctcttctagtagccttcgtacgccacccgaacttcatcggagctctcacaccaaagtggtctaattcc
# catttcgacgatgagacgacccgggactcatacggagttactgcagcctctgcaaaagcgcttgtaccgatcccggctactccttcgaaggaatcgtg
# cttcctccttcatcgtcgccgccgggccatcgtatttactgccacggttgcaaacgccatctag]
# protein sequence = [MLTFLCACVFQRERTVPMTRLAMELLSIYLSPADFSSLLVAFVRHPNFIGALTPKWSNSHFDDETTRDSYGVTAASAK
# ALVPIPATPSKESCFLLHRRRRAIVFTATVANAI]
# end gene g1
###
# start gene g2
Contig38940	AUGUSTUS	gene	6200	6780	0.29	-	.	g2
Contig38940	AUGUSTUS	transcript	6200	6780	0.29	-	.	g2.t1
Contig38940	AUGUSTUS	stop_codon	6200	6202	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig38940	AUGUSTUS	intron	6359	6738	0.74	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig38940	AUGUSTUS	CDS	6200	6358	0.29	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig38940	AUGUSTUS	CDS	6739	6780	0.75	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig38940	AUGUSTUS	start_codon	6778	6780	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggagggcgttatgagtaagcgggagtctcagtctagcgagaacatgcgcggggccgacaatgtagcgggtgaggtcg
# ttcctttagttcgttctgaagagacgggtcgaccatactccttcgggggcggtcctctgaaaccgctcggtggtgaatgggtcatagacatgggatcg
# ccggcattctgttgctacgggtaa]
# protein sequence = [MEGVMSKRESQSSENMRGADNVAGEVVPLVRSEETGRPYSFGGGPLKPLGGEWVIDMGSPAFCCYG]
# end gene g2
###
# start gene g3
Contig38940	AUGUSTUS	gene	6962	8460	0.53	-	.	g3
Contig38940	AUGUSTUS	transcript	6962	8460	0.53	-	.	g3.t1
Contig38940	AUGUSTUS	stop_codon	6962	6964	.	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig38940	AUGUSTUS	intron	7119	7517	0.9	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig38940	AUGUSTUS	intron	7653	8296	0.58	-	.	transcript_id "g3.t1"; gene_id "g3";
Contig38940	AUGUSTUS	CDS	6962	7118	0.9	-	1	transcript_id "g3.t1"; gene_id "g3";
Contig38940	AUGUSTUS	CDS	7518	7652	0.76	-	1	transcript_id "g3.t1"; gene_id "g3";
Contig38940	AUGUSTUS	CDS	8297	8460	0.64	-	0	transcript_id "g3.t1"; gene_id "g3";
Contig38940	AUGUSTUS	start_codon	8458	8460	.	-	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgatgatagcggcgagaaacacatgtttccatgccagcgtaattctggaagaattcggtgtaaagacccggtaccgcg
# gagacgcaggtgctggtgtatgtggctatatgccgttgcagcggggtttatggcggagtaccaccgaggcgatgaagcactggagacttaatttagga
# atagaggagcgtctcatggataaacatgtcagtatggcgggccttttagcggaacacgcggatagccagtgcccgttaatcggtaggaagataataga
# cgcttgcaatcagttcagctgctggggttcgcagagatacaactggacaggtagatttgctggccgggacagagtagaaaccttcaccactgccgaaa
# gtggtcggcacgggcttgtagctggagagtttgtaatctcgatgattggtgaacagtacagcagggacaacactatcgtgtag]
# protein sequence = [MMIAARNTCFHASVILEEFGVKTRYRGDAGAGVCGYMPLQRGLWRSTTEAMKHWRLNLGIEERLMDKHVSMAGLLAEH
# ADSQCPLIGRKIIDACNQFSCWGSQRYNWTGRFAGRDRVETFTTAESGRHGLVAGEFVISMIGEQYSRDNTIV]
# end gene g3
###
# start gene g4
Contig38940	AUGUSTUS	gene	9391	10372	0.44	-	.	g4
Contig38940	AUGUSTUS	transcript	9391	10372	0.44	-	.	g4.t1
Contig38940	AUGUSTUS	stop_codon	9391	9393	.	-	0	transcript_id "g4.t1"; gene_id "g4";
Contig38940	AUGUSTUS	intron	9525	10173	0.46	-	.	transcript_id "g4.t1"; gene_id "g4";
Contig38940	AUGUSTUS	CDS	9391	9524	0.48	-	2	transcript_id "g4.t1"; gene_id "g4";
Contig38940	AUGUSTUS	CDS	10174	10372	0.47	-	0	transcript_id "g4.t1"; gene_id "g4";
Contig38940	AUGUSTUS	start_codon	10370	10372	.	-	0	transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atgcgactgatcggaaaagcggatgaagttcggtgcgaccgttcagctctgcccgccaccatttcatcactagtagtgc
# gtgcttttcgcttcgtgatcggtaagatcaggttacgccatgtgcccgcatgtagatcagcgaaagtaaccgccgccccacacgccccagcgcttgta
# aagggcctagaagtcccagaagaacagttgaggttgaatcagagaccggactctaacggaagtcggcagaggcagtttgctcagtgggagacgattaa
# ggaagtacccaactgtcaggctattgaggagatgtccgttgatgaggccgtatgctaa]
# protein sequence = [MRLIGKADEVRCDRSALPATISSLVVRAFRFVIGKIRLRHVPACRSAKVTAAPHAPALVKGLEVPEEQLRLNQRPDSN
# GSRQRQFAQWETIKEVPNCQAIEEMSVDEAVC]
# end gene g4
###
# start gene g5
Contig38940	AUGUSTUS	gene	14637	15175	0.05	+	.	g5
Contig38940	AUGUSTUS	transcript	14637	15175	0.05	+	.	g5.t1
Contig38940	AUGUSTUS	start_codon	14637	14639	.	+	0	transcript_id "g5.t1"; gene_id "g5";
Contig38940	AUGUSTUS	intron	14730	14869	0.67	+	.	transcript_id "g5.t1"; gene_id "g5";
Contig38940	AUGUSTUS	CDS	14637	14729	0.05	+	0	transcript_id "g5.t1"; gene_id "g5";
Contig38940	AUGUSTUS	CDS	14870	15175	0.96	+	0	transcript_id "g5.t1"; gene_id "g5";
Contig38940	AUGUSTUS	stop_codon	15173	15175	.	+	0	transcript_id "g5.t1"; gene_id "g5";
# coding sequence = [atgcctaagagcctgaaaccattgcatctacagatagaaggatggatagaaaacccaattccagtattttttgttgggg
# ggaggggtataaaaagtatggaggcagcccacatcgatgctgtgatgattttaggagaaaccatggcctttgacgagaactttgattttgggacacag
# agtgcaaccaagcgtatctttaatcttattcaagtgatggcggaacagcgacttacacctccacctcatgaaacgtattcattacatcgtaaaatgtc
# cggatctttcctaatttgcactaaacttgacggcaaagttaattgtaagagactgtttgatgatatttacgctcgatacgagtttggaaaggaatgtg
# aattttgggaggaccaccagaagtaa]
# protein sequence = [MPKSLKPLHLQIEGWIENPIPVFFVGGRGIKSMEAAHIDAVMILGETMAFDENFDFGTQSATKRIFNLIQVMAEQRLT
# PPPHETYSLHRKMSGSFLICTKLDGKVNCKRLFDDIYARYEFGKECEFWEDHQK]
# end gene g5
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370P9T.prfl --predictionStart=0  --predictionEnd=35073  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3894020180911_busco_2432604931_.temp