# 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 /gscratch/scrubbed/samwhite/outputs/20200924_cbai_genome_v1.01_busco/cbai_genome_v1.01.fasta_augustus/config/ ...
# Using protein profile unknown
# --[0..251]--> unknown_A (16) <--[3..7]--> unknown_B (45) <--[0..1]--> unknown_C (9) <--[0..109]--> unknown_D (15) <--[0..2]--> unknown_E (34) <--[2..121]--> unknown_F (13) <--[4..7]--> unknown_G (15) <--[0..38]--> unknown_H (11) <--[0..2]--> unknown_I (9) <--[1..43]--> unknown_J (8) <--[0..15]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_3405cbai_genome_v1.01.fasta_145855183_.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 = 10142, name = contig_3405) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
contig_3405	AUGUSTUS	gene	10200	19080	0.07	+	.	g1
contig_3405	AUGUSTUS	transcript	10200	19080	0.07	+	.	g1.t1
contig_3405	AUGUSTUS	exon	10200	11391	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3405	AUGUSTUS	exon	11446	11861	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3405	AUGUSTUS	exon	16620	17722	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3405	AUGUSTUS	exon	17852	19080	.	+	.	transcript_id "g1.t1"; gene_id "g1";
contig_3405	AUGUSTUS	start_codon	18148	18150	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_3405	AUGUSTUS	CDS	18148	18393	0.99	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_3405	AUGUSTUS	stop_codon	18391	18393	.	+	0	transcript_id "g1.t1"; gene_id "g1";
contig_3405	AUGUSTUS	tts	19080	19080	.	+	.	transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgtacgaaaaaactcaaaatcagtgtacgaaacaactaacaaaacctgggtacgaaacaacttgtgtacgaacctcca
# actactactgctactactactgctgctactgctactgctactactactactgctactgctactactactactactactactactactgctgctgctgc
# tgctactactactactactactactactactactactactacaactgctactcacccggaatgctgtga]
# protein sequence = [MYEKTQNQCTKQLTKPGYETTCVRTSNYYCYYYCCYCYCYYYYCYCYYYYYYYYYCCCCCYYYYYYYYYYYYYNCYSP
# GML]
# end gene g1
###
# command line:
# /gscratch/srlab/programs/Augustus-3.3.2/bin/augustus --codingseq=1 --proteinprofile=/gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/prfl/EOG091G0HAT.prfl --predictionStart=9531  --predictionEnd=19672  --species=fly --progress=true ./tmp/contig_3405cbai_genome_v1.01.fasta_145855183_.temp