# 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
# --[14..105]--> unknown_B (19) <--[40..122]--> unknown_C (29) <--[0..27]--> unknown_D (29) <--[0..29]--> unknown_E (13) <--[1..5]--> unknown_F (28) <--[2..24]--> unknown_G (18) <--[1..24]--> unknown_H (19) <--[4..20]--> unknown_I (14) <--[17..55]--> unknown_K (10) <--[0..273]--> unknown_L (13) <--[0..27]--> unknown_M (17) <--[4..34]--> unknown_N (14) <--[2..5]--> unknown_O (17) <--[2..12]--> unknown_P (17) <--[2..29]--> unknown_Q (14) <--[1..3]--> unknown_R (7) <--[0..6]--> unknown_S (17) <--[4..80]--> unknown_T (27) <--[5..11]--> unknown_U (12) <--[8..24]--> unknown_W (12) <--[19..56]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2971320180911_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 = 12220, name = Contig29713) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig29713	AUGUSTUS	gene	1	1876	0.53	+	.	g1
Contig29713	AUGUSTUS	transcript	1	1876	0.53	+	.	g1.t1
Contig29713	AUGUSTUS	intron	1	216	0.95	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29713	AUGUSTUS	intron	331	1558	0.71	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig29713	AUGUSTUS	CDS	217	330	0.97	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig29713	AUGUSTUS	CDS	1559	1876	0.8	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig29713	AUGUSTUS	stop_codon	1874	1876	.	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gagccacagattatccgcagtctgaacaccagcctggctttctttcttcacgaccttctgagcttcatggaccgaggat
# tcgtcttcaatctcatcgctaactactgcggagccatcgcggagaagatccagatcctctcagaatccaccactctcatgctgctgaggctggacttt
# ctgcggatcgtatgtagccacgagcactacttcccgctcaatctcccgttcgggaccccactgactccgacatccggcaaggtggccagtcccacccc
# cagtatccagagcaccaactctatgtcctcctacacgtctacgtccactctcactgaccgcggtcagttctacgaactcacccttcagttcagacagc
# agcactttttggtggggctggttctgtctgacctcaaggtcgctctcgacacacagtag]
# protein sequence = [EPQIIRSLNTSLAFFLHDLLSFMDRGFVFNLIANYCGAIAEKIQILSESTTLMLLRLDFLRIVCSHEHYFPLNLPFGT
# PLTPTSGKVASPTPSIQSTNSMSSYTSTSTLTDRGQFYELTLQFRQQHFLVGLVLSDLKVALDTQ]
# end gene g1
###
# start gene g2
Contig29713	AUGUSTUS	gene	7683	11842	0.15	-	.	g2
Contig29713	AUGUSTUS	transcript	7683	11842	0.15	-	.	g2.t1
Contig29713	AUGUSTUS	stop_codon	7683	7685	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	intron	7876	8556	0.56	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	intron	8636	9894	0.65	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	intron	10016	10319	0.7	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	intron	10484	10940	0.57	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	intron	10983	11808	0.48	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	CDS	7683	7875	0.76	-	1	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	CDS	8557	8635	0.59	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	CDS	9895	10015	0.73	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	CDS	10320	10483	0.77	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	CDS	10941	10982	0.57	-	2	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	CDS	11809	11842	0.82	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig29713	AUGUSTUS	start_codon	11840	11842	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggtacgtggaggatccgacaggggcggtgcagctctttattatctccccataatggaattggaggaagaatactttt
# tccatgtttgtttacacagggcatattttggaaacctgaacttttttgggggactctccagtgtctgtgccaaggcttcagtcaagttaaaacaagtg
# gagcaggcaaacagagacgccatgtttgtgttcttatcagacgtctggctggaccaggtcaaggtgatagaaaagttaagaatgctatttacgggcta
# ttcggatttccccccgacttgttttatcctgtgtggtaattttatttcttcaccacaagaaagccacagagctaaaatccttaaagggtgtttccgca
# ccttcgtagacctggtgctggagtttcccaacatagcagagaatagccggtttatatttgtaccgggacctcccattcctaattctatcactgaggag
# atcaggaggaagttgcccaattcaaccttcacctctaacccctgtcacatccagtactgtacacaagaaatagtggtcttcagggaggacatcgtcac
# caagatgtgtcgaaactgtgtcaagttcccagcagacaacgacgtcccaactcatgtaagctaa]
# protein sequence = [MVRGGSDRGGAALYYLPIMELEEEYFFHVCLHRAYFGNLNFFGGLSSVCAKASVKLKQVEQANRDAMFVFLSDVWLDQ
# VKVIEKLRMLFTGYSDFPPTCFILCGNFISSPQESHRAKILKGCFRTFVDLVLEFPNIAENSRFIFVPGPPIPNSITEEIRRKLPNSTFTSNPCHIQY
# CTQEIVVFREDIVTKMCRNCVKFPADNDVPTHVS]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370RCD.prfl --predictionStart=0  --predictionEnd=31554  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2971320180911_busco_2432604931_.temp