# 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..100]--> unknown_A (44) <--[4..57]--> unknown_B (13) <--[0..28]--> unknown_C (53) <--[0..3]--> unknown_D (81) <--[0..5]--> unknown_E (22) <--[0..2]--> unknown_F (44) <--[0..74]--> unknown_G (26) <--[2..5]--> unknown_H (39) <--[0..2]--> unknown_I (21) <--[14..102]--
# BUSCO_20180911_busco_2432604931 version. Using default transition matrix.
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
# Looks like ./tmp/Contig4035820180911_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 = 23354, name = Contig40358) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig40358	AUGUSTUS	gene	1	12998	0.03	-	.	g1
Contig40358	AUGUSTUS	transcript	1	12998	0.03	-	.	g1.t1
Contig40358	AUGUSTUS	intron	1	16	0.75	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	154	901	0.97	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	1144	1808	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	1983	2825	0.14	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	2926	3194	0.8	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	3301	8232	0.33	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	8326	9534	0.87	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	9558	9703	0.91	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	9797	9975	1	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	10064	10257	0.73	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	10384	11376	0.92	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	11416	12513	0.89	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	intron	12589	12896	0.86	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	17	153	0.75	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	902	1143	0.97	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	1809	1982	0.17	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	2826	2925	0.43	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	3195	3300	0.58	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	8233	8325	0.85	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	9535	9557	0.91	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	9704	9796	1	-	2	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	9976	10063	1	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	10258	10383	0.73	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	11377	11415	0.92	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	12514	12588	0.96	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	CDS	12897	12998	0.9	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig40358	AUGUSTUS	start_codon	12996	12998	.	-	0	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggcggaattgaggaaactcgggtttgttgggaccataggagaagacgacgaaatagaagtcgagccagagagttctg
# atagcgaggaagacgaccaacaaacatctcaaaaacaaaagaaaaaggcaaagaaaagtgacaatgaatttaacacaaagtttagttttactgatcag
# ggcgtcagactacactcacaaccaacaaagccgtttaatcatgacccagctgccagctttgactttgattttgccatccggcatgctaaacgaaagca
# acatgcaaccacgttagatgaaaagatcgccaaagtcagaaagcaacagaaaaaggtacgcacgaaaggagacaaaccagaagtgttagctgtagaaa
# gtgatgaagacgaaatcgaggaagacgatgaatcttcagatgaggaaatgaggacagacaaaatcaaaacaaaggaaaagaaaaagaagaaaggcaag
# aagaaaaaatcttcttcagatagtgaagaggtagacattctgttgacatctttttcatacgctataagctcgagtgaaaaagaaaaggtggagttttc
# tgagagtgtggattcctatgatgagaaattaacatttcaagacatgaatgtttctcgaccactcatgaagggcctgggtcacatgaacttttccaaac
# ccactccaatccaggcggccaccattccagtcgctctacttgctcgagatctctgtgcctgcgctgttaccggatcgggtaaaactgtggcatttatg
# cttcccattctggaacgattgatgtaccgaactcaacaagaggcggccacgagagtgcttgtgctggtgccgactcgagacttgtttattctgaattt
# tacaggtggattagacgttaaagcacaggaagcagccctacgcatgaatccagatatcgtcatagcaactcccggtagactgatcgatcacttacaca
# atgctccgaacttctctctcagaaacatagaaatcctagtgttggatgaagcagacaggatgttggacgagtacttcgctgagcagatgaatgaaatc
# attcgtcagtgtgccaaatcccgacagacgatgttgttttctgcgaccatgacggaagccgtacaggatctcgcctctgtctcactcaagcagccggt
# caaaatatttgtcaaccagaacacagatgtcgcccttgggctccggcaggagttcatcaggatacgagccaacagagagggggagagggaggccatca
# tagcctccctggtcagccggaccttccgagaccactgtattgtgttcatacagacaaagaagcaggcgcacagaatgcatattgttctgggcttactg
# ggcgtcaacgtgggcgagctccatggcaacctgtctcaggcccag]
# protein sequence = [MAELRKLGFVGTIGEDDEIEVEPESSDSEEDDQQTSQKQKKKAKKSDNEFNTKFSFTDQGVRLHSQPTKPFNHDPAAS
# FDFDFAIRHAKRKQHATTLDEKIAKVRKQQKKVRTKGDKPEVLAVESDEDEIEEDDESSDEEMRTDKIKTKEKKKKKGKKKKSSSDSEEVDILLTSFS
# YAISSSEKEKVEFSESVDSYDEKLTFQDMNVSRPLMKGLGHMNFSKPTPIQAATIPVALLARDLCACAVTGSGKTVAFMLPILERLMYRTQQEAATRV
# LVLVPTRDLFILNFTGGLDVKAQEAALRMNPDIVIATPGRLIDHLHNAPNFSLRNIEILVLDEADRMLDEYFAEQMNEIIRQCAKSRQTMLFSATMTE
# AVQDLASVSLKQPVKIFVNQNTDVALGLRQEFIRIRANREGEREAIIASLVSRTFRDHCIVFIQTKKQAHRMHIVLGLLGVNVGELHGNLSQAQ]
# end gene g1
###
# start gene g2
Contig40358	AUGUSTUS	gene	13766	19428	0.04	+	.	g2
Contig40358	AUGUSTUS	transcript	13766	19428	0.04	+	.	g2.t1
Contig40358	AUGUSTUS	start_codon	13766	13768	.	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	intron	13811	13984	0.36	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	intron	14127	14974	0.52	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	intron	15078	15456	0.73	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	intron	15560	16447	0.91	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	intron	16512	17998	0.61	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	intron	18109	19233	0.45	+	.	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	CDS	13766	13810	0.33	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	CDS	13985	14126	0.37	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	CDS	14975	15077	0.83	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	CDS	15457	15559	0.68	+	1	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	CDS	16448	16511	0.92	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	CDS	17999	18108	0.64	+	2	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	CDS	19234	19428	0.45	+	0	transcript_id "g2.t1"; gene_id "g2";
Contig40358	AUGUSTUS	stop_codon	19426	19428	.	+	0	transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgaagctggttctggtcggtccatggaaaagctgtaaacaccggatacccaaccaactgagctatctggccaccagca
# atcgaacctggctgagtcagtggtcaacggcaccaaatgaaacaggtagggagaaaatgcaacggaccagacgtgatttgaactcgggccccctgaat
# ctccagtcaggacggaaagtagcagtagacgcgtccatgtgcatataccagttcctgattgctgtaagacaagatgggagtaacttaatgagtgaaga
# tggagaaactacaagtcatttgatgggaatgttctacagaactatccgtatggtggagaatggcatgaaacctgtgtatgtatttgatggcaaacctc
# cagaaatgaagtccggtgagcttgctaaacgaaaggaaagaagagaagaggctcagaaacagctggaaaaagcagaggaagcaggtgatgaagagaat
# atagaaaaatttaatagaagactggtaaaagtttcaaaacaacacaatgaagaatgcaaagaacttctgaagttcatgggaattccttacatcaataa
# attgcacattgctcacaattacctgtaccgaggtgatgaattgtttacacaggctccaggtgaagcggaggctcaatgtgctgctctggtaaaagccg
# ggaaagtgtttgccaccgggacagaggatatggacgccctgacgttcggtaccaccgttctgctgaggaatctgacggtcgccgaagccaggtag]
# protein sequence = [MKLVLVGPWKSCKHRIPNQLSYLATSNRTWLSQWSTAPNETGREKMQRTRRDLNSGPLNLQSGRKVAVDASMCIYQFL
# IAVRQDGSNLMSEDGETTSHLMGMFYRTIRMVENGMKPVYVFDGKPPEMKSGELAKRKERREEAQKQLEKAEEAGDEENIEKFNRRLVKVSKQHNEEC
# KELLKFMGIPYINKLHIAHNYLYRGDELFTQAPGEAEAQCAALVKAGKVFATGTEDMDALTFGTTVLLRNLTVAEAR]
# end gene g2
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370FWQ.prfl --predictionStart=0  --predictionEnd=39539  --species=BUSCO_20180911_busco_2432604931 ./tmp/Contig4035820180911_busco_2432604931_.temp