Error in Unassigned Taxa Filtering

[Mehrdad (Meha)]

Hello Dear Admins,
I am having this error for removing the unassigned taxa. I double-checked file names, column name and also I checked parameters. I could not fix it. I found the discussion below, but it was not helpful to do that.

https://forum.qiime2.org/t/qiime-taxa-filter-table-error/3947/5

I followed the recommended protocol in the forum but not worked.

Thanks for your assistance!

[colinbrislawn (Colin J Brislawn)]

Hello again Meha,

Thank you for posting the error. I noticed that the error message mentioned whitespace, and tells you one of your columns has white space in it (like spaces, tabs).

See if you can find the white space shown in the error message example (I found it, you can too!), then see if you can remove it from the metadata file.

Colin

[Mehrdad (Meha)]

Dear Colin,
Thanks for replying!

I used the the metadata in demultiplexing plugin and taxonomy bar plot visualization step. If it had a problem, I would be warned at first steps. Amway, I checked the metadata but I did not find a whites pace honestly. Do you have any idea? I am suspicious to the bug mentioned in the discussion.
https://forum.qiime2.org/t/qiime-taxa-filter-table-error/3947/5

Do you believe this bug fixed? If it is there, what way is to solve this?

[colinbrislawn (Colin J Brislawn)]

I’m not totally sure if the bug it fixed.

However, I think there might be some whitespace in your metadata file based on the error. Specifically, there is a whitespace at the end of the taxonomy line in at least one of the columns.

Like this:

...uncultured bacterium '
the whitespace is here ^

Do you see it now? Try to remove it every trailing whitespace let us know how it goes.

Colin

[Mehrdad (Meha)]

Dear Colin,

I am sharing my header of metadata. There is no any item called column taxon. I have just barcodes'- and primers' sequences in metadata plus time points. that's all. I have no microbial taxa or taxonomy inside it.

I hope is would be enough! if you need more info ask me please.

Thanks

[Mehrdad (Meha)]

By the way, if there is whitespace, it is not my fault. It shows Qiime2 generating it wrongly. It was not manipulated by myself.

I tried this command one more time. I received some lines; maybe help you detect it.

[llenzi (Luca)]

Hi @Mehrdad,
In the context of the command you using, the ‘taxonomylibA.qza’ is the metadata file, in the sense that it contains more information regarding the features in the ‘TableDenoisedLibA.qza’.

If you export/convert the data in the ‘taxonomylibA.qza’ you will find the column taxon.

However, please be careful: this may be not your fault but is not Qiime2 (or its developer) fault either. It is related to the Silva taxonomy file you are using. If you open the taxonomy file (you downloaded by Silva) you will find the space at the end of the taxonomy in here too. It is a good practice to preprocess this taxonomy file to remove the blanks before importing it into Qiime2 artefact. Some Qiime2 plug-in may be insensitive to these (as you used it previously without any issue) but others, such as ‘qiime taxa filter-table’ you are using are.

Best wishes,
Luca