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.
Welcome to the forums!
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.
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.
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.