# 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..250]--> unknown_A (6) <--[0..5]--> unknown_B (43) <--[0..40]--> unknown_C (15) <--[1..5]--> unknown_D (92) <--[0..113]--
# fly version. Using default transition matrix.
# Looks like ./tmp/Contig5197420180911_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 = 14510, name = Contig51974) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# start gene g1
Contig51974	AUGUSTUS	gene	4842	13576	0.01	-	.	g1
Contig51974	AUGUSTUS	transcript	4842	13576	0.01	-	.	g1.t1
Contig51974	AUGUSTUS	tts	4842	4842	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	exon	4842	5096	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	exon	6370	6478	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	stop_codon	6473	6475	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	intron	6479	8860	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	intron	8946	9884	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	intron	10046	10157	0.02	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	intron	10207	10346	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	intron	10406	11166	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	intron	11266	11951	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	intron	11971	13521	0.01	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	CDS	6473	6478	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	CDS	8861	8945	0.01	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	exon	8861	8945	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	CDS	9885	10045	0.04	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	exon	9885	10045	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	CDS	10158	10206	0.01	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	exon	10158	10206	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	CDS	10347	10405	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	exon	10347	10405	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	CDS	11167	11265	0.01	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	exon	11167	11265	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	CDS	11952	11970	0.01	-	1	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	exon	11952	11970	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	CDS	13522	13568	0.02	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	exon	13522	13576	.	-	.	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	start_codon	13566	13568	.	-	0	transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	protein_match	6476	6478	0.955	-	0	target "unknown_D[92..92]"; target_start 82; transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	protein_match	8861	8945	7.38	-	1	target "unknown_D[63..91]"; target_start 82; transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	protein_match	9885	10045	9.07	-	0	target "unknown_D[10..63]"; target_start 82; transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	protein_match	10158	10184	12.6	-	0	target "unknown_D[1..9]"; target_start 82; transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	protein_match	10194	10206	10.6	-	1	target "unknown_C[11..15]"; target_start 64; transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	protein_match	10347	10378	9.61	-	0	target "unknown_C[1..11]"; target_start 64; transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	protein_match	10379	10405	6.52	-	0	target "unknown_B[35..43]"; target_start 21; transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	protein_match	11167	11265	13.9	-	0	target "unknown_B[2..34]"; target_start 21; transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	protein_match	11952	11954	4.62	-	0	target "unknown_B[1..1]"; target_start 21; transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	protein_match	11955	11970	2.31	-	1	target "unknown_A[1..6]"; target_start 15; transcript_id "g1.t1"; gene_id "g1";
Contig51974	AUGUSTUS	protein_match	13522	13523	1	-	0	target "unknown_A[1..1]"; target_start 15; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgacagattacgttactcccaatctctggtatggacaactgttcatatgttttacggtcttcacgccagaagacctca
# tgaatatgcagcattgtaacctgttgtgcctgccagaaaactaccagatgaaatattacttctaccatggtctgtcttggccccagctctcgtatgtt
# gcagaagatgaagaaggacatatagtaggatatgtattagccaaaatggaggaagatccagaggattctgttccacatggacatatcacatcattggc
# ggtgaagcggtctcaccggcgactcgggctggcgcagaagttgatggatcaagcgtcgaggggaatgattgaatgcttcgatgctcagtatgtctcac
# tccatgttagaaagagtaaccgggcggctctacatctctacaaaaacacactcaaattctcagtaagtgaaatagaacctaaatattatgcagatgga
# gaagatgcctacgcgatgaggagaaatctcggcgaatttcgagagaaggtctga]
# protein sequence = [MTDYVTPNLWYGQLFICFTVFTPEDLMNMQHCNLLCLPENYQMKYYFYHGLSWPQLSYVAEDEEGHIVGYVLAKMEED
# PEDSVPHGHITSLAVKRSHRRLGLAQKLMDQASRGMIECFDAQYVSLHVRKSNRAALHLYKNTLKFSVSEIEPKYYADGEDAYAMRRNLGEFREKV]
# sequence of block unknown_D    82 [VPHGHITSLAVKRSHRRLGLAQKLMDQASRGMIECFDAQYVSLHVRKSNRAALHLYKNTLKFSVSEIEPKYYADGEDAYAMRRNLGEFREKV] 174
# sequence of block unknown_C    64 [GHIVGYVLAKMEEDP] 79
# sequence of block unknown_B    21 [TPEDLMNMQHCNLLCLPENYQMKYYFYHGLSWPQLSYVAEDEE] 64
# sequence of block unknown_A    15 [ICFTVF] 21
# end gene g1
###
# command line:
# /augustus/bin/augustus --codingseq=1 --proteinprofile=eukaryota_odb9/prfl/EOG09370TBD.prfl --predictionStart=0  --predictionEnd=31259  --species=fly ./tmp/Contig5197420180911_busco_2432604931_.temp