Error when trying to merge 2 dataset from 2 runs

Dear all,

I have 2 runs (the samples are different between runs but I expect same features) and after doing demux, dada2 and assign taxonomy to each dataset I am trying to combine the 2 datasets. I am doing it using:
qiime feature-table merge on the 2 tables (using sum option)
and then
qiime feature-table merge-taxa on the 2 taxonomy files.
The problem is that, when I try to remove mitochondrial and chloroplast sequences using:
qiime taxa filter-table --i-table merged-table.qza --i-taxonomy merged-taxonomy.qza --p-exclude mitochondria,chloroplast --o-filtered-table merged-table_nomito_nochloro.qza
I get the following error:
Plugin error from taxa:
All features ids must be present in taxonomy, but the following feature ids are not:
then there is a huge list of taxonomies, which I actually have in the merged-taxonomy files.
Could you please help me to understand what I am doing wrong?

Thanks a lot

Cheers

Niccolò

Have you exported the merged taxonomy file? I recommend doing so to make sure that those taxonomies are actually present.

You should also do the same to the taxonomy files that you merged. Either you have merged the wrong taxonomy files or there may be a bug in the merge-taxa method.

Please let us know what you find! Thanks!

Thanks for the reply.
Yes I have exported the taxonomy files and there is no problem apparently with those files. The merged taxonomy file doesn’t get created so I cannot check it. There may be a bug in the merge-taxa method, not sure.
Anyway, I managed to merge the datasets beforehand so I could circumvent this issue and proceed with the analyses.

Thanks for your assistance anyway

Best
Niccolò

What about this file?

Glad to hear you could circumvent. Please send us your files if you can, though — it will help us determine if there is indeed a bug with merge-taxa. Thank you!

Oh sorry, you are right, actually the merged taxonomy gets created, the problem arises when I try to use that merged taxonomy to filter out mitochondrial and chloroplast sequences from the merged table.

Sure, here are my files
merged-table.qza (906.6 KB)
merged-taxonomy_sil.qza (316.3 KB)

Here are the 2 taxonomy files that are merged:
taxonomy_sil.qza (366.9 KB)
taxonomy_sil2.qza (60.6 KB)
with this command:
qiime feature-table merge-taxa --i-data taxonomy_sil2.qza --i-data ../silva/taxonomy_sil.qza --o-merged-data merged-taxonomy_sil.qza

These are the tables that get merged:
table.qza (859.9 KB)
table2.qza (45.6 KB)
using the command:
qiime feature-table merge --i-tables table2.qza --i-tables ../silva/table.qza --o-merged-table merged-table.qza (i tried both with default and sum methods)

hope it helps

Cheers

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Hi @alfanon,
Thanks again for sharing your files. I've spent some time troubleshooting, and have been unable to reproduce your error. Using your command, with merged-taxonomy.qza updated to merged-taxonomy_sil.qza (your actual filename), QIIME2 2018.11 happily produces a FeatureTable. You were working in v18.4, so I'm not sure whether I’ve got different files than you were using, or whether it is version-related. You might try a more current version next time you use this workflow.

I also checked the provenance information in your file. Your merged-table.qza is an exact copy of your table2.qza. This is a red flag that your files may have gotten disorganized, but I’m not entirely clear on your question or what your provenance tree should look like, and that’s making it difficult for me to troubleshoot. Feel free to let us know if you have any further questions or insight on this one.

Happy :qiime2:-ing!
Chris

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