# 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
# --[28..520]--> unknown_C (21) <--[0..1]--> unknown_D (27) <--[1..12]--> unknown_E (26) <--[19..59]--> unknown_G (14) <--[5..7]--> unknown_H (32) <--[0..26]--> unknown_I (20) <--[14..77]--> unknown_K (34) <--[0..35]--> unknown_L (27) <--[2..25]--> unknown_M (8) <--[21..64]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4179920180911_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 = 7411, name = Contig41799) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig41799	AUGUSTUS	gene	1	6530	0.85	-	.	g1
Contig41799	AUGUSTUS	transcript	1	6530	0.85	-	.	g1.t1
Contig41799	AUGUSTUS	intron	1	361	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig41799	AUGUSTUS	intron	526	2498	0.93	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig41799	AUGUSTUS	intron	2656	2807	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig41799	AUGUSTUS	intron	2908	6374	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig41799	AUGUSTUS	CDS	362	525	0.97	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig41799	AUGUSTUS	CDS	2499	2655	0.97	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig41799	AUGUSTUS	CDS	2808	2907	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig41799	AUGUSTUS	CDS	6375	6530	0.94	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig41799	AUGUSTUS	start_codon	6528	6530	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgacacgaagagttctaccgctcatcatggcaagtgttgtggtaccgattgagggacagaagccattattcgccaagc
# cggcgggccagaccggaatacaagctgtaggctcgctgttcaatcctcttccagtgtcggtggcatctcagagtccgattttgaatacaataacagat
# gaaattttgcaagtggaaagcagctacaaaagtccgctggatcaagttgattttattaaatcccagtttgagttgaaagattacagagatttcttcct
# catcgttcacaacatagatggagttatgttacgtccagaaaaagtacaaaatatcctaagtttactgagccagattcggggattccacgtcgtagcgt
# ccattgaccacattaacgctcctctcagtaagtccagacaggatgagacatcttatgagaactcgctgttggtacaacagacgggatccctggccctc
# agctccatgtcccacgtcatgaaaagcttgaccaccaatgctaaacagatattcctgttgctggccaaacatcagattgagaacaaggatagcagtac
# ctatacag]
# protein sequence = [MTRRVLPLIMASVVVPIEGQKPLFAKPAGQTGIQAVGSLFNPLPVSVASQSPILNTITDEILQVESSYKSPLDQVDFI
# KSQFELKDYRDFFLIVHNIDGVMLRPEKVQNILSLLSQIRGFHVVASIDHINAPLSKSRQDETSYENSLLVQQTGSLALSSMSHVMKSLTTNAKQIFL
# LLAKHQIENKDSSTYT]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370GEO.prfl --predictionStart=0  --predictionEnd=20650  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4179920180911_busco_2432604931_.temp