# 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..422]--> unknown_A (34) <--[0..1]--> unknown_B (66) <--[1..7]--> unknown_C (42) <--[0..4]--> unknown_D (47) <--[0..0]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig62520180911_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 = 22489, name = Contig625) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig625	AUGUSTUS	gene	1	5062	0.12	-	.	g1
Contig625	AUGUSTUS	transcript	1	5062	0.12	-	.	g1.t1
Contig625	AUGUSTUS	intron	1	1828	0.44	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig625	AUGUSTUS	intron	1924	2231	0.96	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig625	AUGUSTUS	intron	2410	4922	0.34	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig625	AUGUSTUS	CDS	1829	1923	0.63	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig625	AUGUSTUS	CDS	2232	2409	0.96	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig625	AUGUSTUS	CDS	4923	5062	0.3	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig625	AUGUSTUS	start_codon	5060	5062	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgaaaaggccgggattggccgtggccatgctggaccgaggtttgaatacaactcagacggtccacgaacttccagaaa
# atcttctgagatgggaccgaggattgtactacgttgctggtctaggcagatgtccaaaacagtttggtccatactttgtggaaccagtcattgccgga
# cttgaccctaagacctttgaacctttcattgcctcgatggatttgattggttgtcccatggtcacggacgatttcgttgtcagtggtacttgttcaga
# acagatgtatggaatgtgtgaatctgtctgggaacccaacatggatccacaggagttgtttgagtcgatatcacaggcgctgttgaatgcagtggacc
# gtgatgcagtgtcaggatggggaggaatcgtccatatcat]
# protein sequence = [MKRPGLAVAMLDRGLNTTQTVHELPENLLRWDRGLYYVAGLGRCPKQFGPYFVEPVIAGLDPKTFEPFIASMDLIGCP
# MVTDDFVVSGTCSEQMYGMCESVWEPNMDPQELFESISQALLNAVDRDAVSGWGGIVHI]
# end gene g1
###
# start gene g2
Contig625	AUGUSTUS	gene	9260	9514	0.32	-	.	g2
Contig625	AUGUSTUS	transcript	9260	9514	0.32	-	.	g2.t1
Contig625	AUGUSTUS	stop_codon	9260	9262	.	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig625	AUGUSTUS	CDS	9260	9514	0.32	-	0	transcript_id "g2.t1"; gene_id "g2";
Contig625	AUGUSTUS	start_codon	9512	9514	.	-	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgacatgcagcatgcattccgcaaacaacgatcctgcaaatctcaacatcctcaccatcaacgaccaggtgaaaggac
# tcaatcggcaatcctcggctaactccgctacgctccgtatatacctcggatgtgaatgtgtagggatatgcatcgatttgatacatttctccgccgga
# agtacctgtttactcattccactccgcgtggactgttccttcggctgcagacgactttctcgcattgatgcagtttag]
# protein sequence = [MTCSMHSANNDPANLNILTINDQVKGLNRQSSANSATLRIYLGCECVGICIDLIHFSAGSTCLLIPLRVDCSFGCRRL
# SRIDAV]
# end gene g2
###
# start gene g3
Contig625	AUGUSTUS	gene	14872	20648	0.17	+	.	g3
Contig625	AUGUSTUS	transcript	14872	20648	0.17	+	.	g3.t1
Contig625	AUGUSTUS	start_codon	14872	14874	.	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig625	AUGUSTUS	intron	15153	18033	0.31	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig625	AUGUSTUS	intron	18315	18439	1	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig625	AUGUSTUS	intron	18637	19343	0.99	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig625	AUGUSTUS	intron	19474	20391	1	+	.	transcript_id "g3.t1"; gene_id "g3";
Contig625	AUGUSTUS	CDS	14872	15152	0.57	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig625	AUGUSTUS	CDS	18034	18314	1	+	1	transcript_id "g3.t1"; gene_id "g3";
Contig625	AUGUSTUS	CDS	18440	18636	0.99	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig625	AUGUSTUS	CDS	19344	19473	1	+	0	transcript_id "g3.t1"; gene_id "g3";
Contig625	AUGUSTUS	CDS	20392	20648	1	+	2	transcript_id "g3.t1"; gene_id "g3";
Contig625	AUGUSTUS	stop_codon	20646	20648	.	+	0	transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atggagatcgggaagaactctagtttagatgcaagggtggtacaggcacccaactacatgcgtatcggtgaccagagta
# tgcaattccatcctcagcagttccacaaacccacgtatgattcacagcagtcgttagaaacggacggggaggtgatgatggaagaggtgtctcctgac
# gttatcaacaatgactccgggtttttttctcaggggatagtttcagaccgagaaccacaaagtctgtcctctggaatcaaagtcaagacaagcacaac
# acaaaggccacaggagccccgccacatagacatgtccagatcagtcttcctggccacggaatataaaatggaccatccaaagagagggagagccctca
# tcatcaacaacatgaactatgctgatgtccgtcagagaccggagcgagaggaatcgatctacgatgcgtcggctatgcaaaatctgctcgagtgtctg
# aagtttagtccagtaacccaaaggatgggtcacaaaagcatggtgatcactgacgtgtcttcaaagcagttagaggaaataattcaagatgtgaccaa
# ccctgcactgaatgatttcagcgactgtgattgcttcatgatggttgtccttagttacgggatagatggcgctataatgtgttgtgaaggagaaaagg
# acaagcttatccccgtcgaacaagttgtcgaaaagttcaaagctgacaaatgcccctccttggctatgaaaccaaaactttttttcatgcagttgtgt
# ccagctttttcctacaacatagctgactcaataggaggaaggggtggtgccaaaacaatggaacctgaaatccggaagattccaaccgattccgatat
# cttggttcaaatctcgaatctgccaggttcctatggctggtacgaagatgacaatgccctctcctggtacattgagggattgaaagaaacattacaga
# agaactgttacgaccctttacggcagggtcaaaggtcaaaggaaattaatgacattctcctccatgtgaacagactgtatatcaagaagctgagagaa
# cagggcatctgtcctaataaacactactcggcaccagccattacatcaacactgacaaaggatttgtattttcttcctaaaagatga]
# protein sequence = [MEIGKNSSLDARVVQAPNYMRIGDQSMQFHPQQFHKPTYDSQQSLETDGEVMMEEVSPDVINNDSGFFSQGIVSDREP
# QSLSSGIKVKTSTTQRPQEPRHIDMSRSVFLATEYKMDHPKRGRALIINNMNYADVRQRPEREESIYDASAMQNLLECLKFSPVTQRMGHKSMVITDV
# SSKQLEEIIQDVTNPALNDFSDCDCFMMVVLSYGIDGAIMCCEGEKDKLIPVEQVVEKFKADKCPSLAMKPKLFFMQLCPAFSYNIADSIGGRGGAKT
# MEPEIRKIPTDSDILVQISNLPGSYGWYEDDNALSWYIEGLKETLQKNCYDPLRQGQRSKEINDILLHVNRLYIKKLREQGICPNKHYSAPAITSTLT
# KDLYFLPKR]
# end gene g3
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370R3M.prfl --predictionStart=0  --predictionEnd=22489  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig62520180911_busco_2432604931_.temp