# 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..53]--> unknown_A (44) <--[4..5]--> unknown_B (12) <--[5..8]--> unknown_C (49) <--[11..22]--> unknown_D (14) <--[4..25]--> unknown_E (18) <--[1..3]--> unknown_F (17) <--[1..59]--> unknown_G (9) <--[6..23]--> unknown_H (40) <--[2..12]--> unknown_I (8) <--[0..1]--> unknown_J (18) <--[20..81]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4278320180911_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 = 29745, name = Contig42783) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig42783	AUGUSTUS	gene	1	16163	0.01	-	.	g1
Contig42783	AUGUSTUS	transcript	1	16163	0.01	-	.	g1.t1
Contig42783	AUGUSTUS	intron	1	375	0.78	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	intron	480	832	0.84	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	intron	935	1034	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	intron	1107	1664	0.96	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	intron	1778	2926	0.55	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	intron	2936	4079	0.38	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	intron	4187	4994	0.51	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	intron	5225	5767	0.43	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	intron	5840	8390	0.33	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	intron	8533	12701	0.47	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	intron	12810	15252	0.63	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	intron	15397	16038	0.56	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	376	479	0.71	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	833	934	0.85	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	1035	1106	0.98	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	1665	1777	1	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	2927	2935	0.55	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	4080	4186	0.44	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	4995	5224	0.42	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	5768	5839	0.62	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	8391	8532	0.81	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	12702	12809	0.49	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	15253	15396	0.58	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	CDS	16039	16163	0.83	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig42783	AUGUSTUS	start_codon	16161	16163	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgggcgtactacgagaatttaagcctcggccggaccggcacacaggaactggatatctgtcaaacttccgcccagctg
# ttaattacaatcagcgtctggatgaggtggataacccagtcttaagccaagggttttcggtccaatccactccccagtatgggtttttggtccactcc
# cggagcggatggaccgaaaaacccttggctagcgaagatggtgggatcgggaggaatcagcgtttcacaatcagcctgatattgcaaatgatagtctt
# gttgaagaagtctggtagccggacacctcgaattgaattggaagagattgggccatcactggacctcgtcatcagaagaaccaagctggcttcagagg
# acttagtcttgttgaagaagtctggtaccggacacctcgaattaattggaagagattgggccatcactggactcgtcatcagaagaaccaagctggcc
# tcagaggacctgtacaaaagggccctcaaacagcccaaaaccatcaaagtcatcagtttagtgcacaatgaggagcacgttgccttgacaacgataaa
# gccgctcgagaagaaccgaaagatgggaccccttccacagggcagtagaaatgtacacatcatggccagtcaagggccggacatcagcatgatgaagt
# tttataataccactaactctactacctatgggcggtactacgagaagtttaagcctcggcctggacggcacacaggaactggatatctgtcaaacttc
# cgcccagctgtgtattacaatcagcgtctggatgaggtggataacccagtcttaagtcgaattatgtgcacgagattaccacgtgtgactgaagcttc
# actaccaagaaaactccggagcagaacctctgccaagaaatgttcaccagaaaggatcaggatttagattcatgtggacctcaccaataaaactgtgg
# gcccccaggaggagagtggcttcacacacgcctataatgtagaacccattacgtacatcccagggtccccacacaaaaacgagctaccaggttgggcc
# accggccgtcctactggagttagcagaatgaagaccgatttcttgaggtcagaatatcccaagggtgatgaaccattgccggggttgtcccatggttc
# tgagcgcggtacagggttcaccagagagaaggccaaacctatgtatgtcaacagaatcatggcagatgcctatgacagagcagagaacattcccccca
# tgaggttggataggacaaagaaagtggacccaacggagtatctaaacatgcagaatcccaacaaccactccag]
# protein sequence = [MGVLREFKPRPDRHTGTGYLSNFRPAVNYNQRLDEVDNPVLSQGFSVQSTPQYGFLVHSRSGWTEKPLASEDGGIGRN
# QRFTISLILQMIVLLKKSGSRTPRIELEEIGPSLDLVIRRTKLASEDLVLLKKSGTGHLELIGRDWAITGLVIRRTKLASEDLYKRALKQPKTIKVIS
# LVHNEEHVALTTIKPLEKNRKMGPLPQGSRNVHIMASQGPDISMMKFYNTTNSTTYGRYYEKFKPRPGRHTGTGYLSNFRPAVYYNQRLDEVDNPVLS
# RIMCTRLPRVTEASLPRKLRSRTSAKKCSPERIRIXIHVDLTNKTVGPQEESGFTHAYNVEPITYIPGSPHKNELPGWATGRPTGVSRMKTDFLRSEY
# PKGDEPLPGLSHGSERGTGFTREKAKPMYVNRIMADAYDRAENIPPMRLDRTKKVDPTEYLNMQNPNNHS]
# end gene g1
###
# start gene g2
Contig42783	AUGUSTUS	gene	16586	23455	0.01	+	.	g2
Contig42783	AUGUSTUS	transcript	16586	23455	0.01	+	.	g2.t1
Contig42783	AUGUSTUS	start_codon	16586	16588	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig42783	AUGUSTUS	intron	16667	20279	0.29	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig42783	AUGUSTUS	intron	20379	21901	0.63	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig42783	AUGUSTUS	intron	22093	23346	0.82	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig42783	AUGUSTUS	CDS	16586	16666	0.36	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig42783	AUGUSTUS	CDS	20280	20378	0.67	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig42783	AUGUSTUS	CDS	21902	22092	0.63	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig42783	AUGUSTUS	CDS	23347	23455	0.05	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig42783	AUGUSTUS	stop_codon	23453	23455	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgctagcgaacgccctaggtcttgctgcaagtcatcatgtggaaatatcgagggctacaaagttaaagtacggtcaat
# acaccaattcagaagccctgacacgatcagcagacacccagttgacccttgaccctcgaacttgtgatcccaaaatcgatatgggtcatctactccaa
# catctgatgagcctcccgattccaccatcttcgctagccaagggttttcggtccactccgctccccataatggagaggggagtggaccaaaaacccat
# actggggagcggattggaccgaaaacccttggctagcgaagatggtggaatcgggaggcatcagcgtttcacaatcagcctgatattgcaaatgatca
# agacggcacacagacgcgcacggacaaaaggtgatgccagaaatgctcttggccttcggggcttacaggtgaggctaagaaagtttgagaaatacgcg
# tggatttga]
# protein sequence = [MLANALGLAASHHVEISRATKLKYGQYTNSEALTRSADTQLTLDPRTCDPKIDMGHLLQHLMSLPIPPSSLAKGFRST
# PLPIMERGVDQKPILGSGLDRKPLASEDGGIGRHQRFTISLILQMIKTAHRRARTKGDARNALGLRGLQVRLRKFEKYAWI]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370NBT.prfl --predictionStart=0  --predictionEnd=32883  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4278320180911_busco_2432604931_.temp