error observed during "aligning all feature sequences"

[fengyuchengdu]

error observed during "aligning all feature sequences"

[SionBayliss]

Dear Feng Yu,

That is odd. Unfortunately, I didn't make the error message terrible informative. That specific error message does not kill the script so it is likely that it has only failed to align a single gene g037324 as indicated by the error below. If you could inspect that file and identify if there are any obvious issue with it (e.g. unalignable characters, odd formatting, blank sequences) it would be much appreciated.

You can do this by re-aligning that problematic gene. If you provide a modified PIRATE.gene_families.tsv fie to align_feature_sequences.pl which only contains a single line for g037324 then it will realign that problem gene:

perl ./PIRATE_script_path/align_feature_sequences.pl --dosage 1.25 -i PIRATE.gene_familes.MODIFIED.tsv -g ./PIRATE/modified_gffs/ -o PIRATE/feature_sequences/ -p 1

If you comment out (put a #) before the line below in align_feature_sequences.pl then you should be able to view the intermediate file created by this script which will contain the sequences to be aligned:

unlink "$output_dir/$cluster.fasta";

change to: (and save)

#unlink "$output_dir/$cluster.fasta";

This should give you some insight into why the script is failing on that gene.

I hope that helps,
Sion

[fengyuchengdu]

Thanks much for your swift reply. These do help me a lot.