# 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..546]--> unknown_A (20) <--[0..7]--> unknown_B (20) <--[0..1]--> unknown_C (34) <--[0..3]--> unknown_D (18) <--[4..11]--> unknown_E (60) <--[0..2]--> unknown_F (59) <--[0..1]--> unknown_G (22) <--[0..7]--> unknown_H (35) <--[0..1]--> unknown_I (85) <--[2..14]--> unknown_J (67) <--[6..19]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig72120180911_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 = 22156, name = Contig721) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig721	AUGUSTUS	gene	885	2255	0.88	-	.	g1
Contig721	AUGUSTUS	transcript	885	2255	0.88	-	.	g1.t1
Contig721	AUGUSTUS	stop_codon	885	887	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig721	AUGUSTUS	CDS	885	2255	0.88	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig721	AUGUSTUS	start_codon	2253	2255	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcacgttgtttacataaaatgctaacacttaatggtagattgaagtcacgttttgtgtcagagatcggaatgttta
# caacacacactagagcattctctttctcgttctcaaagttgagtgataaaccattttgcaatgttggtactataggacatgttgaccacggaaaaaca
# actcttacagccgcaattaccaaagttttgtcagaggaactgggaacaacgaaaactgtgaaatttgatgaaatcgacaaagcaccagaggaaaagaa
# aagaggaattaccataaacgctgctcacattagtttcgagtcaaacaaacgacaatatgctcacaccgactgcccaggccatatagactttataaaaa
# acatgatcactggagcggcacagatggacggagctattcttgttgtggctgcaacagaaggcacgatgccccaaactcgtgaacatgtactacttgcc
# aaacagattggtgtgaaacatatagtggtttacattaataaagttgatgctgcggatgaagaaatggccgagctctgtgaaattgaagtccaaatgtt
# actggatgaatatggatataagggttctgaagttcccgttgttcgaggatctgcattaaatgcattgaatggtgaaaatgaagaaattggcaaaaaat
# ctattttgaagttagtcaacattcttgatgaatatattccaataccagatcgagatttgtcagccccatatgttttacccatagaatcagcagtaaaa
# attccaagtcgaggtacagttgttgttggaacattaaaagatggtgtaataactaaaggtgatgctgctgaaatcatcgggcagggcgtttccataca
# gagttcagtaactgatattgaagtgtttcacgagtctgtaccaaagctttttgcagggcaaaatgctggagttcttttgaaaggaattaaacagacta
# acattaaccgtggtatgtttttagtgaaaccaaatacagccactcagcattcctatttctgtgccaaagtttatgttctgacgagagaggaaggaggt
# cgcacaaaaccagttagaaatgaatatcaacaacaactattttgttcattgtggtccatgggatgtatcatatatttgccagaggacatacccatgat
# aatgccaggggacactgcagatgttaaagtattattacgacagccgatgattttaaaggtcggacaacagttcactattcgtgaaaatcgaatttcct
# ctgtgactggaattgtgacagaaattttacctcctattgatgtagaaatcaaaggttttacttttctgaagcctctaccttcagttaagattgagggg
# aaaaggaaaagaaagtga]
# protein sequence = [MARCLHKMLTLNGRLKSRFVSEIGMFTTHTRAFSFSFSKLSDKPFCNVGTIGHVDHGKTTLTAAITKVLSEELGTTKT
# VKFDEIDKAPEEKKRGITINAAHISFESNKRQYAHTDCPGHIDFIKNMITGAAQMDGAILVVAATEGTMPQTREHVLLAKQIGVKHIVVYINKVDAAD
# EEMAELCEIEVQMLLDEYGYKGSEVPVVRGSALNALNGENEEIGKKSILKLVNILDEYIPIPDRDLSAPYVLPIESAVKIPSRGTVVVGTLKDGVITK
# GDAAEIIGQGVSIQSSVTDIEVFHESVPKLFAGQNAGVLLKGIKQTNINRGMFLVKPNTATQHSYFCAKVYVLTREEGGRTKPVRNEYQQQLFCSLWS
# MGCIIYLPEDIPMIMPGDTADVKVLLRQPMILKVGQQFTIRENRISSVTGIVTEILPPIDVEIKGFTFLKPLPSVKIEGKRKRK]
# end gene g1
###
# start gene g2
Contig721	AUGUSTUS	gene	3841	12129	0.04	+	.	g2
Contig721	AUGUSTUS	transcript	3841	12129	0.04	+	.	g2.t1
Contig721	AUGUSTUS	start_codon	3841	3843	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	intron	3872	8077	0.34	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	intron	8818	9043	0.97	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	intron	9104	9230	0.95	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	intron	9284	9525	0.99	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	intron	9671	9712	0.51	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	intron	9872	9929	0.53	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	intron	10120	10308	1	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	intron	10797	10888	0.92	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	intron	11242	11605	0.86	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	intron	11619	11727	0.73	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	intron	11823	12014	0.42	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	3841	3871	0.65	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	8078	8817	0.69	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	9044	9103	0.99	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	9231	9283	0.96	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	9526	9670	0.98	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	9713	9871	0.53	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	9930	10119	1	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	10309	10796	0.92	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	10889	11241	0.52	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	11606	11618	0.84	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	11728	11822	0.5	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	CDS	12015	12129	0.41	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig721	AUGUSTUS	stop_codon	12127	12129	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgagatcgaccataaaaaccgaggccccgtcagtggtagaaaatccagaaaatggatcgtcagtaagtcaacaagtga
# acaccgattctctttccggttctgttgctcaactgtccttcaataaccagaatcatgaaacagtaaaggaaaacaagaagccctgttatacgtttgag
# aagtacggaagttgcagatttgggaatagttgtcgttatctccatgcattgccaaaggaattgcatctaaagaaaccaaactcgaccaagaattccaa
# gtctgacaaaaagtctaataatgattccaaaaaccttggtcaccgtcaacagaaccaagaaagaagagaaagaagacggatctgccactattaccagg
# aaggctattgtcagaaggggaacaactgcagatttcaccatccagatggcctggatcaagtagctaatttggatgtcatcctaagagaggacaaggaa
# caaacagggaagaaagatgcctgtgttgaaagcgtggcatcgggccaaagcaatgataaaaaggagcaaaacaggaagttcacaccaaaagcggggca
# gagaaaaattgtacccagaccagttcagcctgtgaaggagtttcaaagagatggcttacgggagaaagaggttgagaatctccgatcgactgaaattg
# aacaactgaaaaagagactggcagcctccagcttagaggtcatcactgacgatgaagaaagcttttgtgtacagtttgatttttcatccagtgaccca
# gattggccgtatgatgtggaagtattcaagttacaagtcactataccaaaggaataccctacgaagatgtttggtgttagactctctgatgaacagaa
# tttaccagaaacggtacaaaggtacattgacacttctcttgaggactggataaatacaaagcaggcagaattaatatcagtaggtattgtcagactgg
# agtttagacctttcatgaaatggttggataagaacctggaatctatcgttactggcgctctgaagcagatgactcttcattatttttgtaaaattaaa
# tgtaacagagacagttttgtgcctctgctgaggatcgaacccgggacctctggcacagtagtccagtgctctaccaatcgagccagagctagtaggaa
# gggctgtaaaaaaaaaataaagaagcacaatttgaagaaagagctagatgccaaggcagcagggttgcagtttatacctgcatctaaactacaggaaa
# aagtcaaagcagctgttagcgatgaggaggaagaggaggaggaggaggaagaaggcgaggaggagtgtaaaatgttcggaggagtggtctacagaaaa
# acagaagaggacttcatttacacaggtccgcagcaacagagtgatgagtctgaatcagaagacgatgatttgattgattctgccatcaatgataaaaa
# accagagagggatgaaagacggggaaccgaagtaaagctgaggaacctcacgctaaaggacaatgcttcgacacttacctgtgctacccttaaagtca
# tcattcagtgcgcccgctgtaaaaacaagatggatgtcggcacaccctcggggaggccaaaccttgtgacttgtgggaaatgcagctacccacaggtc
# gtgacctttcgctcagcaatcatgcatcaattttcctcggtagtaggctatctggatttagatgntcaggtcgcgacctttcgctcagcaatcatgca
# tcagttctcctcggtagtaggctatctggatttagatggatgcgttccgtttgatcttatccttcaggactgtgtgttcaagctgggatgctttagtt
# gcaacaaagaaatgaaagccaagagcatggccttcggacaagttaccgatacatggtgttcccactgtcacagcaaaatgaaagtatcggcagagtct
# gtccgttttgctcaacttcttccttcagagcaagatttgggtaagaattgcagatttgtcgtcaacttattgatcctctctgtgtatgtacttgcaga
# attccacttgtctaccgtgttaaaaaaaaatttgattacagtttcagaggaaaagggtctgcacaaaattccagttttgaagccaaagaaaaatgtga
# aagaacccgagatccagctgggctatccattacctaaggatggaacttgtaaacactacaagaaaagctatcgctggttcaggttcccctgttggata
# aggcgttgttgttggctgcaagcagtcgatgacccaagtccgtacagctcactgggaggggggcagatgcaggacaagtctaaaatgggcaggaatga
# tgctcaaaatatgcaggccaatcaaaaactgtgtccaggtaaggctcaggacaaacagaagacatcgactgcgaagaagaacatcaagttacgtcaca
# gtagtcattga]
# protein sequence = [MRSTIKTEAPSVVENPENGSSVSQQVNTDSLSGSVAQLSFNNQNHETVKENKKPCYTFEKYGSCRFGNSCRYLHALPK
# ELHLKKPNSTKNSKSDKKSNNDSKNLGHRQQNQERRERRRICHYYQEGYCQKGNNCRFHHPDGLDQVANLDVILREDKEQTGKKDACVESVASGQSND
# KKEQNRKFTPKAGQRKIVPRPVQPVKEFQRDGLREKEVENLRSTEIEQLKKRLAASSLEVITDDEESFCVQFDFSSSDPDWPYDVEVFKLQVTIPKEY
# PTKMFGVRLSDEQNLPETVQRYIDTSLEDWINTKQAELISVGIVRLEFRPFMKWLDKNLESIVTGALKQMTLHYFCKIKCNRDSFVPLLRIEPGTSGT
# VVQCSTNRARASRKGCKKKIKKHNLKKELDAKAAGLQFIPASKLQEKVKAAVSDEEEEEEEEEEGEEECKMFGGVVYRKTEEDFIYTGPQQQSDESES
# EDDDLIDSAINDKKPERDERRGTEVKLRNLTLKDNASTLTCATLKVIIQCARCKNKMDVGTPSGRPNLVTCGKCSYPQVVTFRSAIMHQFSSVVGYLD
# LDXQVATFRSAIMHQFSSVVGYLDLDGCVPFDLILQDCVFKLGCFSCNKEMKAKSMAFGQVTDTWCSHCHSKMKVSAESVRFAQLLPSEQDLGKNCRF
# VVNLLILSVYVLAEFHLSTVLKKNLITVSEEKGLHKIPVLKPKKNVKEPEIQLGYPLPKDGTCKHYKKSYRWFRFPCWIRRCCWLQAVDDPSPYSSLG
# GGQMQDKSKMGRNDAQNMQANQKLCPGKAQDKQKTSTAKKNIKLRHSSH]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG093704HC.prfl --predictionStart=0  --predictionEnd=22156  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig72120180911_busco_2432604931_.temp