# 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
# --[10..101]--> unknown_B (15) <--[0..1]--> unknown_C (14) <--[10..34]--> unknown_E (71) <--[0..24]--> unknown_F (24) <--[0..1]--> unknown_G (25) <--[11..61]--> unknown_H (63) <--[1..2]--> unknown_I (22) <--[13..37]--> unknown_J (17) <--[2..14]--> unknown_K (31) <--[0..1]--> unknown_L (9) <--[1..4]--> unknown_M (10) <--[0..12]--> unknown_N (16) <--[0..4]--> unknown_O (11) <--[3..49]--> unknown_P (17) <--[1..15]--> unknown_Q (68) <--[8..39]--> unknown_S (27) <--[18..46]--> unknown_U (38) <--[3..20]--> unknown_V (9) <--[0..1]--> unknown_W (23) <--[11..97]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig3589720180911_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 = 12198, name = Contig35897) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig35897	AUGUSTUS	gene	1733	11797	0.04	-	.	g1
Contig35897	AUGUSTUS	transcript	1733	11797	0.04	-	.	g1.t1
Contig35897	AUGUSTUS	stop_codon	1733	1735	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	1823	2319	0.98	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	2437	4307	0.91	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	4531	4753	0.94	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	4828	5258	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	5367	5517	0.7	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	5623	5678	0.84	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	5739	6117	0.33	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	6259	6420	0.69	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	6583	6832	0.98	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	6998	7652	0.52	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	7708	9615	0.8	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	9729	9930	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	9969	10937	0.99	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	intron	11070	11682	0.83	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	1733	1822	0.97	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	2320	2436	0.98	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	4308	4530	0.86	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	4754	4827	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	5259	5366	0.72	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	5518	5622	0.95	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	5679	5738	0.88	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	6118	6258	0.41	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	6421	6582	0.93	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	6833	6997	0.56	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	7653	7707	0.57	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	9616	9728	0.94	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	9931	9968	0.98	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	10938	11069	1	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	CDS	11683	11797	0.28	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig35897	AUGUSTUS	start_codon	11795	11797	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgagacaggatgtttttgatgctcttgttgcttttgagaagaaatctcccactgaggggtcagaagaatcgaagagat
# acgtagaaagaatgatcaagctcggcaggcgaaacggtcttcatctgccctcagaaacacaacaaaagattaaagaaatcaaaaagagaatgagtgat
# ttatccatagatttcagtaaaaacctcaacgaggaaaacacaatccttacctttacaaaggaagagcttgctggagttcctgaagatttcctgaagtc
# tcttgaaaagaatgaagatggcaaattgaaggtgacgttaaagtacccacattatttcccttgcatgaagaaagtgagaaacccagagacgaggaaga
# aactagagacagcctttaactccaggtgtcttgaaccaaatacagccatattagaagaattagtggagcttcgaagtcagaaagctgacatcctgggc
# tttcctacccatgcagcttttattctcgacatgagaatggctaaagaccccgagaaagtgaaaacattcctcgtggacctggcccaaaagctccgccc
# cttacagagtcaagaggtcaaagtcttcctcgactacaagaaagaggagtgcgagaagtacggctatgaatatgatgggaagattaactactgggacc
# tacgatactacatgacgatgacagaagaacgccagtacgcggtggattcgaaccatctgaaggaatatttccccatggaagtggtgaccactggactt
# ttagagatctaccaggaactgctgaatctcaagtttactcaggtgaaagatgtagaagtttggcatccagaggtcaccttggtgagtgaagccataga
# taacaacattttaataaatcaagaaatggaaaacaaacttctgacttcaaatttagtggatttggacaacaggctggaagtattttacatccctattt
# ggaaaaagttaactgctcagtacagtgtagaagatgtctcatcctccaatctcctcggctatttttatctcgacctttatcctcgagagggaaaatat
# ggacatgcagcttgttttggacttcagccgggatgtctgcagccggatggaaaaaggcagatttctgtggctgcaatggtcgccaatttcaccaaacc
# cactgaagataaaccagcactgctgactcacgatgaggttgagacttacttccacgagtttggccatgtcatgcaccagatttgcgctcaatctgaat
# ttgctctgttcagcgtggagagggatttcgtggaggccccgtcccagatgttggagaactggtgctgggagaaagagccgctccggagaatgtccaag
# cattacaaaaccggggaactgattccggacgacctcttggagaaactgatcaagagccggatcgccaacgctgggatgtttaaccttcgacagattct
# cctggggatgtttgatcaaaccattcacacgcagaagaagtggagtgaagtgttctgtatggatatgttctacacacgctttatgaaggagggaatca
# tgagtccaaaagtgggcggggactacagaagatgtatattacgtccaggcggatccatagatgctgcagatatgttgcgcaacttcctgggtcgtgac
# cccacaccagaagctttcctgatcagtaagggactcaatccaaatgcataa]
# protein sequence = [MRQDVFDALVAFEKKSPTEGSEESKRYVERMIKLGRRNGLHLPSETQQKIKEIKKRMSDLSIDFSKNLNEENTILTFT
# KEELAGVPEDFLKSLEKNEDGKLKVTLKYPHYFPCMKKVRNPETRKKLETAFNSRCLEPNTAILEELVELRSQKADILGFPTHAAFILDMRMAKDPEK
# VKTFLVDLAQKLRPLQSQEVKVFLDYKKEECEKYGYEYDGKINYWDLRYYMTMTEERQYAVDSNHLKEYFPMEVVTTGLLEIYQELLNLKFTQVKDVE
# VWHPEVTLVSEAIDNNILINQEMENKLLTSNLVDLDNRLEVFYIPIWKKLTAQYSVEDVSSSNLLGYFYLDLYPREGKYGHAACFGLQPGCLQPDGKR
# QISVAAMVANFTKPTEDKPALLTHDEVETYFHEFGHVMHQICAQSEFALFSVERDFVEAPSQMLENWCWEKEPLRRMSKHYKTGELIPDDLLEKLIKS
# RIANAGMFNLRQILLGMFDQTIHTQKKWSEVFCMDMFYTRFMKEGIMSPKVGGDYRRCILRPGGSIDAADMLRNFLGRDPTPEAFLISKGLNPNA]
# end gene g1
###
# start gene g2
Contig35897	AUGUSTUS	gene	11889	12198	0.2	-	.	g2
Contig35897	AUGUSTUS	transcript	11889	12198	0.2	-	.	g2.t1
Contig35897	AUGUSTUS	stop_codon	11889	11891	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig35897	AUGUSTUS	intron	12054	12198	0.81	-	.	transcript_id "g2.t1"; gene_id "g2";
Contig35897	AUGUSTUS	CDS	11889	12053	0.2	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [gtgcttgctgacaatgattgtgaatatgcagtggtgcggaacaacctggacttcatgcagcatgtttccccggataagg
# atctcagagacgccagtgtggacattgacaaaaaactctccgaatttgacgtggaaatgaggtgtagtgactttgtgtgtctttag]
# protein sequence = [VLADNDCEYAVVRNNLDFMQHVSPDKDLRDASVDIDKKLSEFDVEMRCSDFVCL]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093705E5.prfl --predictionStart=0  --predictionEnd=24553  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig3589720180911_busco_2432604931_.temp