# 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..64]--> unknown_A (27) <--[1..16]--> unknown_B (10) <--[0..34]--> unknown_C (10) <--[0..2]--> unknown_D (20) <--[0..1]--> unknown_E (15) <--[1..3]--> unknown_F (21) <--[0..1]--> unknown_G (33) <--[2..61]--> unknown_H (41) <--[2..11]--> unknown_I (32) <--[0..1]--> unknown_J (18) <--[0..1]--> unknown_K (59) <--[0..20]--> unknown_L (6) <--[2..4]--> unknown_M (60) <--[1..2]--> unknown_N (53) <--[0..6]--> unknown_O (15) <--[0..2]--> unknown_P (28) <--[0..106]--> unknown_Q (48) <--[0..190]--> unknown_R (51) <--[0..1]--> unknown_S (36) <--[4..13]--> unknown_T (32) <--[0..1]--> unknown_U (19) <--[0..17]--> unknown_V (10) <--[2..8]--> unknown_W (21) <--[1..81]--> unknown_X (31) <--[1..11]--> unknown_Y (126) <--[0..2]--> unknown_Z (57) <--[0..2]--> unknown_AA (13) <--[0..5]--> unknown_AB (51) <--[0..3]--> unknown_AC (16) <--[33..133]--> unknown_AD (11) <--[0..1]--> unknown_AE (21) <--[8..42]--> unknown_AG (9) <--[5..13]--> unknown_AH (10) <--[0..1]--> unknown_AI (25) <--[5..18]--> unknown_AJ (7) <--[0..5]--> unknown_AK (18) <--[0..1]--> unknown_AL (42) <--[22..40]--> unknown_AN (11) <--[0..2]--> unknown_AO (13) <--[11..17]--> unknown_AP (19) <--[0..16]--> unknown_AQ (30) <--[13..20]--> unknown_AS (20) <--[0..2]--> unknown_AT (35) <--[0..1]--> unknown_AU (39) <--[0..1]--> unknown_AV (13) <--[3..17]--> unknown_AW (39) <--[3..38]--> unknown_AX (21) <--[2..8]--> unknown_AY (70) <--[0..1]--> unknown_AZ (26) <--[0..1]--> unknown_BA (23) <--[1..56]--> unknown_BB (17) <--[0..2]--> unknown_BC (22) <--[24..131]--> unknown_BE (34) <--[2..5]--> unknown_BF (11) <--[0..1]--> unknown_BG (26) <--[8..42]--> unknown_BH (39) <--[2..68]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig5994620180911_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 = 3791, name = Contig59946) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig59946	AUGUSTUS	gene	1	3791	0.21	+	.	g1
Contig59946	AUGUSTUS	transcript	1	3791	0.21	+	.	g1.t1
Contig59946	AUGUSTUS	intron	1	228	0.85	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	intron	317	733	0.86	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	intron	879	1534	0.5	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	intron	1625	2536	0.48	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	intron	2690	2840	0.74	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	intron	2967	3529	0.85	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	intron	3722	3791	0.9	+	.	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	CDS	229	316	0.85	+	2	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	CDS	734	878	0.54	+	1	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	CDS	1535	1624	0.49	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	CDS	2537	2689	0.69	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	CDS	2841	2966	0.74	+	0	transcript_id "g1.t1"; gene_id "g1";
Contig59946	AUGUSTUS	CDS	3530	3721	0.9	+	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [gctggggaagttgtggaaccattagagtaaattactgcgagattcttgctcaagtcaggcagtttgtggaactaacgag
# gaaaataaaccgcccattggaattggacacagatggcatctggtgtgtcctgccagccacattcccagagaactacgtggtgaaatcaactaatgcta
# aaaaacccaaagtgactgtgtcttacccaggagccatgctcaacatcatggtcaaggatctgttcactaacgaccagtatcaggaactggaagatgcc
# cgagcactgaagtactcggtgcgcagtgaaaactccatcttctttgaggggtttgaggtgaagagaagaggggagttggaactgatcaagatgttcca
# gtcctccgggtttgaagcttttctgaagggcgttacgttggacgagtgctatgcagctgtcgctaaggtggcagactattggctagacgttctcttta
# gcaaggcagaaaacatgccagattccgaattatttgagttgattgcggagaagcgaaacatgtctagaactttggcagactacggcgagcagaaatca
# acatcaatcagcacggctaaacgtctggctgagtttctgggtgaccagatggtgaaggatgccggcctgaactgtcattatgtgatttcgaagaaacc
# cgagggatctcccgtcacggagagagccattcctctagccatcttccaggcagaagccagtgtcaccaaacattacctccgcaagtggctcaagagtc
# ccagcttgtcagattttggaatccgagag]
# protein sequence = [WGSCGTIRVNYCEILAQVRQFVELTRKINRPLELDTDGIWCVLPATFPENYVVKSTNAKKPKVTVSYPGAMLNIMVKD
# LFTNDQYQELEDARALKYSVRSENSIFFEGFEVKRRGELELIKMFQSSGFEAFLKGVTLDECYAAVAKVADYWLDVLFSKAENMPDSELFELIAEKRN
# MSRTLADYGEQKSTSISTAKRLAEFLGDQMVKDAGLNCHYVISKKPEGSPVTERAIPLAIFQAEASVTKHYLRKWLKSPSLSDFGIRE]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370082.prfl --predictionStart=0  --predictionEnd=23724  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig5994620180911_busco_2432604931_.temp