# 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
# --[12..365]--> unknown_A (14) <--[0..23]--> unknown_B (23) <--[0..3]--> unknown_C (15) <--[14..46]--> unknown_E (32) <--[0..12]--> unknown_F (12) <--[0..1]--> unknown_G (49) <--[19..84]--> unknown_J (38) <--[0..66]--> unknown_K (26) <--[0..4]--> unknown_L (8) <--[1..13]--> unknown_M (45) <--[2..7]--> unknown_N (23) <--[1..15]--> unknown_O (9) <--[11..23]--> unknown_P (24) <--[0..27]--> unknown_Q (13) <--[1..17]--> unknown_R (13) <--[1..23]--> unknown_S (7) <--[0..18]--> unknown_T (17) <--[0..17]--> unknown_U (27) <--[10..80]--> unknown_W (26) <--[0..22]--> unknown_X (9) <--[0..595]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5732320180911_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 = 6195, name = Contig57323) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig57323	AUGUSTUS	gene	1973	5257	0.11	-	.	g1
Contig57323	AUGUSTUS	transcript	1973	5257	0.11	-	.	g1.t1
Contig57323	AUGUSTUS	stop_codon	1973	1975	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig57323	AUGUSTUS	intron	2273	3533	0.36	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig57323	AUGUSTUS	intron	3548	4103	0.27	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig57323	AUGUSTUS	intron	4230	4478	0.93	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig57323	AUGUSTUS	intron	4558	5032	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig57323	AUGUSTUS	CDS	1973	2272	0.55	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig57323	AUGUSTUS	CDS	3534	3547	0.28	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig57323	AUGUSTUS	CDS	4104	4229	0.83	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig57323	AUGUSTUS	CDS	4479	4557	0.97	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig57323	AUGUSTUS	CDS	5033	5257	0.59	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig57323	AUGUSTUS	start_codon	5255	5257	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaaggcggggccattaggagtagatctggacttcacttttggttcccgagaaaatcctgctcttctgaatgagttgg
# gactgatcgtgagcaatgtctgcaatgtgattcctgggggcgtggtctgtttcttctcgtcctacgattaccagaaccttgtttatcagcactggcaa
# aagacgggaatcctagccaaactggagaagaaaaagcggatcttccaggagcctaaattgtccagtcaagtggagcaggttctaggagaatattccaa
# atccattcaaaaatccagctgtggaacaggaggcgattttgttttgtgtagtgggagggaaaatgagttgaaggcatcaacttctccgacgatctcag
# gtcgaggtgttacattggtggcatgccgtaccccaacatcaagagcccagaatacagggcaggaactacaggaaaaaatgcagtatttgaattcaaat
# ttcccaaaggacaaagatggacacttgcctggtcaagtacactacgaaaacttgtgtatgaaagccgtcaatcagtctattggccgagccattcgtca
# ccggggagattatgcaaccattctgttgctggataaacgctactgtaaagagaacgtaagaaccaaacttcctacttggataggaaaagatctgcaga
# aaatggagaagtacggaccagccatcgctgccatttcaaagttcttcaggggaaagaaatcagacaatacaacttaa]
# protein sequence = [MKAGPLGVDLDFTFGSRENPALLNELGLIVSNVCNVIPGGVVCFFSSYDYQNLVYQHWQKTGILAKLEKKKRIFQEPK
# LSSQVEQVLGEYSKSIQKSSCGTGGDFVLCSGRENELKASTSPTISGRGVTLVACRTPTSRAQNTGQELQEKMQYLNSNFPKDKDGHLPGQVHYENLC
# MKAVNQSIGRAIRHRGDYATILLLDKRYCKENVRTKLPTWIGKDLQKMEKYGPAIAAISKFFRGKKSDNTT]
# end gene g1
###
# start gene g2
Contig57323	AUGUSTUS	gene	5287	6195	0.4	-	.	g2
Contig57323	AUGUSTUS	transcript	5287	6195	0.4	-	.	g2.t1
Contig57323	AUGUSTUS	stop_codon	5287	5289	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig57323	AUGUSTUS	intron	5990	6195	0.66	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig57323	AUGUSTUS	CDS	5287	5989	0.4	-	1	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [attccgatccagactgaaagccaaaaatttactgtatgtgaagcagatcttgtatatcctgagctgtttggtgagggta
# ctaggtggacggacagacgcaagcgtaattaaacaaacggtcgggaagtccgagtccaaagtgatgacggtgaaccagtttctgtcggatagcggatt
# cgacaacatcaatttgttcaagattttacaatattgtcggaaaagccaaatctcgaaaaaattaaatggttttgtggaaaagtatccaaacaatgagg
# ttgctatagcaacagaaaagaaagaggagagacacacaggaatcacaggtttcttgaaagaaattacgcaaaatgtggaggcctctaattcaactgca
# gaaatacagaagccaatcgacagcagggggagtgaggaagccgtcgtaatgaggtcaccattgatgcatatcgagggattttttgcctccctaacaaa
# cgctgacaaagatggaagaattgtgctaaccaaacaaccattgctgagcaactgttcattgaaatttttgctgatgaaccctgccgtccatttcaggg
# atttactgtccgaggccaggtcagtggtggtggggggggaaccatgcagccgatggacgagttcaaacaacagctgttttttgcagctggaattggtc
# ccgagaaaattcatgaatattcatgtggtcatgtga]
# protein sequence = [FRSRLKAKNLLYVKQILYILSCLVRVLGGRTDASVIKQTVGKSESKVMTVNQFLSDSGFDNINLFKILQYCRKSQISK
# KLNGFVEKYPNNEVAIATEKKEERHTGITGFLKEITQNVEASNSTAEIQKPIDSRGSEEAVVMRSPLMHIEGFFASLTNADKDGRIVLTKQPLLSNCS
# LKFLLMNPAVHFRDLLSEARSVVVGGEPCSRWTSSNNSCFLQLELVPRKFMNIHVVM]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093707RF.prfl --predictionStart=0  --predictionEnd=25550  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5732320180911_busco_2432604931_.temp