align.seqs subfiles in default Directory

mothur bugs
1

Unsure what the source of the error is. Using align.seqs(fasta=current, reference=silva.v4.fasta), I get this:

Reading in the /usr/analysis/tools/mothur/silva.v4.fasta template sequences… DONE.
It took 6 to read 14956 sequences.
[ERROR]: Could not open /usr/analysis/tools/mothur/silva.v4.8mer


which is exceptionally odd, as silva.v4.8mer is there, and universally readable. Is there are requirement for mothur to be able to WRITE to silva.v4.8mer? The command finishes, so it's obviously not an unrecoverable error.

Thank you,
=Matt

2

Mothur rewrites the “shortcut” reference files it creates with each new version, so write permissions are necessary on the file.