Error during Heatmap Generation

Dear expert,

I want to create a heatmap for my analysis, but I have an error for it. First I filter my table based on this page:
then I filter my table based on the frequency only to obtain desired visualized taxa in my heatmap and I get artifact file as attached below. After that, I try to generate heatmap using this command:
qiime feature-table heatmap
--i-table filter-table-heatmap.qza
--m-sample-metadata-file metadata1.tsv
--m-feature-metadata-file metadata1.tsv
--p-metric braycurtis
--o-visualization heatmap.qzv

then I got the following error message:
(1/2) Missing option "--m-sample-metadata-column".
(2/2) Missing option "--m-feature-metadata-column".

After I got those message, I retried using this command:
qiime feature-table heatmap
--i-table filter-table-heatmap.qza
--m-sample-metadata-file metadata1.tsv
--m-sample-metadata-column source
--m-feature-metadata-file metadata1.tsv
--m-feature-metadata-column source
--p-metric braycurtis
--o-visualization heatmap.qzv

then I still got the error message as follows:
Plugin error from feature-table:
Cannot visualize an empty table.
Debug info has been saved to /tmp/qiime2-q2cli-err-ogp2kysh.log

Please help me to solve that problem. Did I wrong with my command? or I have some mistakes with my metadata file or filtered table? I also attached my metadata file for further consideration.
Thank you for your kind response.

filter-table-heatmap.qza (56.0 KB) metadata1.tsv (245 Bytes)

Hi @fhermanto96!

Step 1: check out the error message:

Step 2: verify that table is empty (feature-table summarize):

Step 3: check provenance to see what kind of filtering was done

Apparently you filtered in 4 separate steps. I would go back and double check which step is producing the empty table, then we can chat more about why its creating an empty table.

Keep us posted!


Honestly I got this table after 4 times of filtering step (I’m beginner using QIIME2 and I just learnt it by my self from some forum topics). I did that because I want to eliminate some taxa from my table according to taxonomic assignment, so I decided to filter it using p-exclude. There were 3 taxa I would exclude for my downstream analysis, so I did it one by one until I got a table before filter it based on frequency (and filter-table-heatmap.qza artifact was a final one after filtering by its frequency) :sweat_smile:. Does it a problem for my final table artifact?

Thank you for your suggestion @thermokarst

Dear @thermokarst, after I recheck my previous table (which I used for filter-feature step as an input), it had a value inside it (not an empty table).filter-table-fix.qza (58.6 KB) filter-table-fix.qzv (445.9 KB)

After that I directed to filter-feature step using those table using following command:
qiime feature-table filter-features
--i-table filter-table-fix.qza
--p-min-frequency 100
--p-max-samples 20
--m-metadata-file metadata1.tsv
--o-filtered-table filter-table-heatmap.qza
then I check it using feature-table summarize and got the same result as you did filter-table-heatmap.qzv (405.1 KB) . Is there some mistakes with my parameter during filter-feature?
Thank you for your help.

Thanks for the details @fhermanto96!

I think so!

Here you appear to be providing Sample metadata when filtering Features - the sample IDs will not match any of your feature IDs, which is why the table is filtering to nothing. Drop that line and try again!


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