qiime2R error while classifying with Silva132 but not Green Genes

I am receiving the following error when trying to view my classification.qza artifact in R after classifying with the pre-trained Silva132 classifier.

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 12706 did not have 3 elements

When I classify the same data with with the pre-trained green genes classifier, I am able to view the data in R by running the same command.

Hello Jake,

Welcome to the forums! :qiime2:

Strange! I bet it’s something to do with taxa names in the classification, but I’m not sure.

Let’s see if the qiime2R developer has seen this before. @jbisanz any advice?


P.S. Other Bioinformatics Tools is definitely the right category for this topic, so I removed the second post. :+1:

Hi Jake, there might be some weird character on this line. Could you possibly post this line, or send me the artifact to debug? The fix will be easy once I know what is on that line.

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Hi Jordan, I have attached the artifact.

silva.classification.qza (880.5 KB)

The problem has to do with #s in the taxonomy string. However, I made an update a while back to account for this. If you reinstall from github you should be able to read the file no problem. I am just in the middle of doing an update this morning so if you wait a few hours you will have the most recent version.

dd877ca311e2298472a80ae41c8d42f0	D_0__Bacteria;D_1__Bacteroidetes;D_2__Ignavibacteria;D_3__OPB56;D_4__uncultured bacterium #0319-6E22;D_5__uncultured bacterium #0319-6E22;D_6__uncultured bacterium #0319-6E22	0.9781462091131308

I apologize for not having the most recent version of qiime2R installed. Thank you for all of your help and I will install the most recent version this afternoon.