# 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..79]--> unknown_B (31) <--[0..2]--> unknown_C (32) <--[7..14]--> unknown_D (26) <--[0..1]--> unknown_E (28) <--[1..4]--> unknown_F (22) <--[0..2]--> unknown_G (57) <--[2..3]--> unknown_H (33) <--[1..3]--> unknown_I (11) <--[0..1]--> unknown_J (33) <--[0..1]--> unknown_K (47) <--[0..2]--> unknown_L (56) <--[0..6]--> unknown_M (65) <--[9..16]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig2148020180911_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 = 11729, name = Contig21480) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig21480	AUGUSTUS	gene	4890	10516	0.08	-	.	g1
Contig21480	AUGUSTUS	transcript	4890	10516	0.08	-	.	g1.t1
Contig21480	AUGUSTUS	stop_codon	4890	4892	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	intron	4956	6351	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	intron	6442	6655	0.53	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	intron	6794	7510	0.52	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	intron	7639	7888	0.75	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	intron	7951	8677	0.84	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	intron	8815	9297	0.98	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	intron	9477	10014	0.48	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	intron	10115	10459	0.32	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	CDS	4890	4955	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	CDS	6352	6441	0.99	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	CDS	6656	6793	0.53	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	CDS	7511	7638	0.8	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	CDS	7889	7950	0.85	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	CDS	8678	8814	0.9	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	CDS	9298	9476	0.48	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	CDS	10015	10114	0.46	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	CDS	10460	10516	0.46	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig21480	AUGUSTUS	start_codon	10514	10516	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgggagatgttgaaaatcgaccttattctacagtagagtcggttcgagaaatcgagattgatgagaagacagtggtgt
# catcaacagagccttgtctttggaaaagtcccaagaaaatggtgcggtcattggtgaggtgtcattggagtagagctgaatttttgtccaatgttgga
# ggcgtgggaattgatttggatgtcgccaaaaactttcaacgaatccttcaaaaacaaggactgaaattcaaaatggacaccaaagttaccagtgcctc
# tagagtcggagacaaaattaaagtggccattgagggagtgaaaaaccaaaaacaggaagagatagaatgtgatgtgttactggtgtgtatcggtagga
# ggccatacactaacagcattggtttagaggaagtaggaattcccaaggacagccgaggaagagtagaggtcaactcacgattccaaactgttgttcca
# agtgtttatgcaattggtgactgcatacatggaccaatgttggcacacaaagcagaggatgagggcatcatctgtgtagagggaatgatgggaggggc
# cgtgcatcttgactataactgtgtcccctcagttatttacacacacccagaagtggcctgggtaggcaagacagaggagcaactcaaggaggagggag
# ttgtatacaaaattggaaaatttcccctaattgccaacagtcgtgccaaaacaaatgacgacaccgatggatttgtgaaagttttagcagataaagaa
# acagataaattactgggttgtcatttcataggttcagtggctggagaattaatcaatgaagctgttttagccatggaatatggagcatcgtgtgaaga
# cattgccagagtttgtcatgcacatcctacggtatcagaagccttacgagaagccaacttagcagcatatgcagggaaagccattaactgctag]
# protein sequence = [MGDVENRPYSTVESVREIEIDEKTVVSSTEPCLWKSPKKMVRSLVRCHWSRAEFLSNVGGVGIDLDVAKNFQRILQKQ
# GLKFKMDTKVTSASRVGDKIKVAIEGVKNQKQEEIECDVLLVCIGRRPYTNSIGLEEVGIPKDSRGRVEVNSRFQTVVPSVYAIGDCIHGPMLAHKAE
# DEGIICVEGMMGGAVHLDYNCVPSVIYTHPEVAWVGKTEEQLKEEGVVYKIGKFPLIANSRAKTNDDTDGFVKVLADKETDKLLGCHFIGSVAGELIN
# EAVLAMEYGASCEDIARVCHAHPTVSEALREANLAAYAGKAINC]
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370AJP.prfl --predictionStart=0  --predictionEnd=29519  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig2148020180911_busco_2432604931_.temp