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padlocbio / padloc

Locate antiviral defence systems in prokaryotic genomes
MIT License
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-p meta option is missing #7

Closed genomesandMGEs closed 2 years ago

genomesandMGEs commented 2 years ago

Hi,

Thanks for developing padloc, it looks cool! I was running this tool on several mobile elements, which tend to be quite smaller than chromosomes, and I got this error:

Error: Sequence must be 20000 characters (only 5237 read). (Consider running with the -p meta option or finding more contigs from the same genome.)

ERROR: prodigal failed\n

Warning: ideally Prodigal should be given at least 100000 bases for training. You may get better results with the -p meta option.

However, the -p meta option is not available in the command line. Could you please fix this?

Thank you.

leightonpayne commented 2 years ago

Thanks for trying out PADLOC. According to Prodigal's own documentation, it's not recommended for use on sequences < 100 kbp. To fix this error, we've added a check for sequence length that will reject sequences < 100 kbp.

If you still want to use Prodigal, then you can run it before using PADLOC with the -p meta / -p anon option, or use some other gene prediction software before using PADLOC.