# 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..80]--> unknown_A (27) <--[0..1]--> unknown_B (50) <--[0..32]--> unknown_C (72) <--[4..42]--> unknown_D (22) <--[0..2]--> unknown_E (33) <--[8..20]--> unknown_G (44) <--[0..1]--> unknown_H (29) <--[1..232]--> unknown_I (22) <--[0..35]--> unknown_J (28) <--[3..4]--> unknown_K (16) <--[1..15]--> unknown_L (15) <--[6..28]--> unknown_N (22) <--[0..1]--> unknown_O (13) <--[0..28]--> unknown_P (19) <--[0..63]--> unknown_Q (20) <--[0..14]--> unknown_R (21) <--[0..1]--> unknown_S (13) <--[0..3]--> unknown_T (11) <--[1..15]--> unknown_U (23) <--[0..5]--> unknown_V (12) <--[10..32]--> unknown_X (26) <--[0..23]--> unknown_Y (12) <--[4..5]--> unknown_Z (41) <--[0..58]--> unknown_AA (27) <--[0..9]--> unknown_AB (24) <--[0..17]--> unknown_AC (16) <--[4..89]--> unknown_AD (20) <--[0..44]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig482620180911_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 = 9347, name = Contig4826) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig4826	AUGUSTUS	gene	1	8714	0.02	-	.	g1
Contig4826	AUGUSTUS	transcript	1	8714	0.02	-	.	g1.t1
Contig4826	AUGUSTUS	intron	1	1093	0.69	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	intron	1274	1703	0.48	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	intron	1860	2210	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	intron	2419	2663	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	intron	2813	3697	0.62	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	intron	3782	4145	0.95	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	intron	4301	4534	0.67	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	intron	4678	4929	0.98	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	intron	5021	5345	0.6	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	intron	5443	6167	0.64	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	intron	6270	8708	0.13	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	CDS	1094	1273	0.93	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	CDS	1704	1859	0.7	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	CDS	2211	2418	0.97	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	CDS	2664	2812	0.98	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	CDS	3698	3781	0.77	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	CDS	4146	4300	0.67	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	CDS	4535	4677	0.66	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	CDS	4930	5020	0.61	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	CDS	5346	5442	0.62	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	CDS	6168	6269	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	CDS	8709	8714	0.12	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig4826	AUGUSTUS	start_codon	8712	8714	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgatgccttccacacctcagttgtccccccaggaagagcaggagaagcttttggaggagggaatcaccatagttaaaa
# accagtcattccagatgaaaagatgtctggacaaagggaagttaatggatggactaaagcatgcatcaacaatgcttggcgaactgagaacttcactg
# ttatctccaaagagctactacgaactatagctttacctctgtgatgagttccaaaaggggaggaaagttgcagatctgtatgaactcgttcaatatgc
# aggaaatattgttccaaggctctacctactgatcacagtgggagtggtgtacattaaatctaatgaactttcccgtaaagacattctgaaagacttgg
# tggaaatgtgtcgaggtgttcagcatcccttgaggggcctctttctgagaaattacctgctgacttagatgaacaagttgtgggttcgtatgcagcat
# cagggtcacacgcgggatcgcacaaagcgtgaacaggagagacgagaactccgaattttggttggaaccaatcttgttcggctcagtcagctggagtg
# cattgatatggacaagtacaaaaaggtggttctccccgcggtgttagaacaagtggtgtcttgccgggatcccatcgctcaggagtatttgatggagt
# gtattatccagaatcgacccgacatgcctccggaggatattgtttccctccaggtggcgctggtgaacctggcactgaagtgttacccagataaagta
# cactatgttgacaaagtgctagaaacgactgaggatatcttcaacagacacaatctagaccatttggagtatggcagtctggtttccaaggaactgat
# gagactgatgaagatcccagtcgattcttacaacaacattctgactgttctggaactacaacactttggtcccatttttgattattttgattaccaga
# gcaggaaaatcatgtgctcctatctcatcaacaatgttctggaaaatgaaacttgtatacccacgcaagaacaggtggacagcatccttaacattgtg
# aatgtccttgtacaagaccagagtgatcagccaacagaaccagacgacccagaagactttgctgaggagcaagtgctcatgggaagatttatacatct
# actccaagcagaagatccaaatcaacaatatttagatgaaaactgggagaagaaatgccaaaagatcttccagttctgccatcagactataggagcgt
# taatcaaggcggacatggcagagatgccactcagactgtttctacagggagcaatgacagctggagagattgaatttgaaaaccacgaaactgtagcc
# tatgaattcatgtcacag]
# protein sequence = [MMPSTPQLSPQEEQEKLLEEGITIVKNQSFQMKRCLDKGKLMDGLKHASTMLGELRTSLLSPKSYYELXLYLCDEFQK
# GRKVADLYELVQYAGNIVPRLYLLITVGVVYIKSNELSRKDILKDLVEMCRGVQHPLRGLFLRNYLLTXMNKLWVRMQHQGHTRDRTKREQERRELRI
# LVGTNLVRLSQLECIDMDKYKKVVLPAVLEQVVSCRDPIAQEYLMECIIQNRPDMPPEDIVSLQVALVNLALKCYPDKVHYVDKVLETTEDIFNRHNL
# DHLEYGSLVSKELMRLMKIPVDSYNNILTVLELQHFGPIFDYFDYQSRKIMCSYLINNVLENETCIPTQEQVDSILNIVNVLVQDQSDQPTEPDDPED
# FAEEQVLMGRFIHLLQAEDPNQQYLDENWEKKCQKIFQFCHQTIGALIKADMAEMPLRLFLQGAMTAGEIEFENHETVAYEFMSQ]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093703WD.prfl --predictionStart=0  --predictionEnd=25442  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig482620180911_busco_2432604931_.temp