# Error with filter-features-conditionally on picrust2 outputs
**URL:** https://forum.qiime2.org/t/error-with-filter-features-conditionally-on-picrust2-outputs/27343
**Category:** PICRUSt2
**Tags:** picrust, filtering, feature-table
**Created:** [August 9, 2023, 2:27pm UTC](https://forum.qiime2.org/t/error-with-filter-features-conditionally-on-picrust2-outputs/27343 "2023-08-09T14:27:36Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@vimh](https://forum.qiime2.org/u/vimh)
#### Post date: [August 9, 2023, 2:27pm UTC](https://forum.qiime2.org/t/error-with-filter-features-conditionally-on-picrust2-outputs/27343/1 "2023-08-09T14:27:36Z")
Hello everyone,
Im not sure this is the best channel to ask my thing but maybe you can help me. Im trying to use the filter-features-conditionally option on picrust output ko-metagenome table. I want to retain the most frequent KO numbers in order to do a heatmap.
> qiime feature-table filter-features-conditionally
> --i-table ko-table.qza
> --p-abundance 0.9 \
> --p-prevalence 0 \
> --o-filtered-table filtered-ko-table.qza
It is confusing to me because when I use the above command my table is not filtered at all, the resulting "filtered-ko-table.qza" contains exactly the same information that "ko-table.qza". On the other hand, when i use the below command, my table is empty. All the features are filtered out. I can see it with the feature-table summarize option and because in the first case when I try to draw the heatmap the table is too large and otherwise the plugin says that it can´t draw anything from an empty table (obviously).
> qiime feature-table filter-features-conditionally
> --i-table ko-table.qza
> --p-abundance 0.9 \
> --p-prevalence 0.1 \
> --o-filtered-table filtered-ko-table.qza
Maybe I don´t really understand the plugin, I´m trying to retain the 10% most abundant features in my table, and I only need them to be very abundant in one single sample in order to compare with the others. I don´t know if picrust2 output tables have different format or the plugin is not reading well the table or what is happening there, but i definitively need your help.
Thank youy very much,
Víctor
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### Author:  [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)
#### Post date: [August 9, 2023, 4:05pm UTC](https://forum.qiime2.org/t/error-with-filter-features-conditionally-on-picrust2-outputs/27343/2 "2023-08-09T16:05:39Z")
Hi @vimh,
This action, as called in your second command, will retain all features that are present at least 90% abundance in at least 10% of your samples, so it's working as expected (it's unlikely that any features meet that criteria). Your first command will retain all features that are present at least 90% abundance in at least 0% of your samples - so that one should keep everything. Does that make sense?
I don't think we have an easy way to do exactly what you're looking for here. If you set `--p-prevalence` to one divided by your total number of samples, that should let you retain features based on abundance in one sample. You could then experiment with `--p-abundance` settings to try to keep the most abundant features.
Alternatively, if you're comfortable with Python programming, you can use the [Python 3 API](https://docs.qiime2.org/2023.5/interfaces/artifact-api/) to load your feature table as a `pandas.DataFrame` and perform the filtering with pandas.
I'll keep this post queued in case other developers have ideas on how to achieve this that I'm not thinking of.
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### Author:  [@vimh](https://forum.qiime2.org/u/vimh)
#### Post date: [August 10, 2023, 8:01am UTC](https://forum.qiime2.org/t/error-with-filter-features-conditionally-on-picrust2-outputs/27343/3 "2023-08-10T08:01:56Z")
Hello Greg,
Thank you so much for your help. I wasn´t understanding perfectly how the plugin were working and was trying to fit the plugin to my needs. I will try to do this outside qiime, or calculating a threshold frequency in order to use filter-features with --p-where parameter filtering out frequencies below the threshold.
Effectively, any feature is too frequent to pass the 1% filter. I used --p-abundance 0.001 and the table was filtered.
Thank you again and sorry for the time loss.
Víctor
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### Author:  [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)
#### Post date: [August 10, 2023, 4:23pm UTC](https://forum.qiime2.org/t/error-with-filter-features-conditionally-on-picrust2-outputs/27343/4 "2023-08-10T16:23:58Z")
Sounds good - feel free to post if you run into additional questions!