No gff created

[marco91sol]

Hi,

I am using your script "infernal-tblout2gff.pl" for transforming a *tblout file in gff. But, no output file has been created. The command that I used is the following:

perl ~/Scripts/infernal-tblout2gff.pl --cmscan --fmt2 --desc genome.tblout genome.tblout.gff3

[nawrockie]

@marco91sol : if you attach your .tblout file I will try to reproduce the problem and figure out what is going on.

[nawrockie]

Actually, based on your command, it looks like you are providing too many command line arguments. The script outputs to STDOUT so to save to genome.tblout.gff3 try this:

perl ~/Scripts/infernal-tblout2gff.pl --cmscan --fmt2 --desc genome.tblout > genome.tblout.gff3

Note the > before genome.tblout.gff3. Let me know if that fixes the issue or not.