mothur

Problem with dist.seqs

Below is what I get when I try to run dist.seqs. Not sure how to fix it.

"mothur > dist.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta, cutoff=0.03)
[ERROR]: stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta is blank, aborting.
You have no current fastafile and the fasta parameter is required.
Using 8 processors.

[ERROR]: did not complete dist.seqs."

I skipped over the mock community stuff but everything before it ran fine.

Thanks for the help.

Hi mbeebe -

Thanks for your question! What command did you run to generate stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta? This error makes me think you used get.groups to get the mock rather than remove.groups. If you didn’t use the mock community, then you could skip the remove.groups step and instead use stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta as input to dist.seqs.

Pat

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