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missing the DNA fasta output file #26
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It seems that prodigal -i <genome.fa> -d <nucleotide.fa> -a <prot.faa> -o <genome.gff> -f gff -p meta will give the exact same output as the prodigal run in ViralRecall cmd = "prodigal -p meta -i "+genome_file" -a "+protein_file" I just need the nucleotide.fa output |
Yes - "-a" gives the protein output and "-d" provides the nucleic acid
sequence. You have the right command.
Does that answer your question?
Frank
…On Tue, Feb 27, 2024, 8:23 PM Andrian Gajigan ***@***.***> wrote:
It seems that
prodigal -i <genome.fa> -d <nucleotide.fa> -a <prot.faa> -o <genome.gff>
-f gff -p meta
will give the exact same output as the prodigal run in ViralRecall
cmd = "prodigal -p meta -i "+genome_file" -a "+protein_file"
I just need the nucleotide.fa output
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Yes. Thanks Frank! |
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Thank you for creating this tool! Helps me a lot.
I noticed I was missing this output file when I ran ViralRecall:
*.fasta: The DNA coding sequence of the predicted proteins from Prodigal
Running, for instance,
python viralrecall.py -i bin.10.fa -p bin.10 -t 8 -c
would only give me
bin.10.faa
bin.10.full_annot.tsv
bin.10.markerout
bin.10.pfamout
bin.10.summary.tsv
bin.10.vogout
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