Differential abundance analysis

Dear all,

I performed Taxonomy classification and taxonomic analyses referring to hitdb. I performed a differential abundance analysis using ancom and i received this message :
Plugin error from composition:

Unable to allocate 82.0 TiB for an array with shape (3357899, 3357899) and data type float64

Debug info has been saved to /tmp/qiime2-q2cli-err-1fcfq_sh.log

Thanks

Hi @M_F!

I’m not really sure what you’re trying to do here, can you please give us more details? Also, filenames don’t really mean anything in QIIME 2, since you can name a file anything you want, so it would be helpful if you kept that in mind when elaborating on your description a bit more. Thanks!

Hello @thermokarst

Thanks for the reponse. Sorry the question is wrong. I performed a differential abundance analysis using ancom and i received this message :
Plugin error from composition:

Unable to allocate 82.0 TiB for an array with shape (3357899, 3357899) and data type float64

Debug info has been saved to /tmp/qiime2-q2cli-err-1fcfq_sh.log

What can i do ? Thanks for your help

Thanks for clarifying, @M_F.

The error message is here:

You have a huge amount of features in your FeatureTable: 3,357,899. ANCOM is crashing because the amount of memory necessary for that calculation is 82.0 TiB. That kind of memory is basically impossible to come by on a single machine:

https://www.quora.com/What-is-the-most-RAM-a-computer-has-ever-had?share=1

2 TB of RAM on a single computer is about as good as it gets right now, so realistically there is no way for you to perform ANCOM on 3.3 million features.

Keep us posted! :t_rex:

2 Likes

@thermokarst

Thank you so much for the response.
i run the job sample per sample.
I tried to filter and collapse the table, the job was run with success. However actually i have a problem to run the ancom test with the command --m-metadata-column
qiime composition ancom
–i-table comp-gut-table-l6.qza
–m-metadata-file sample-metadata.tsv
–m-metadata-column Disease
–o-visualization l6-ancom-subject.qzv
i received this message when i used the aforementioned command line
Plugin error from composition:

All values in grouping are unique. This method cannot operate on a grouping vector with only unique values (e.g., there are no ‘within’ variance because each group of samples contains only a single sample).

Debug info has been saved to /tmp/qiime2-q2cli-err-axqj1bma.log

In the table i have a column called Disease (Healthy vs Affected) and i would like that ancom test will be performed for SAM.1 since i run the job for each sample separately.
What can i do to run Ancom test for the column Disease taking into consideration the data specific to only SAM.1 or sample 1 in the first row ?
Thanks a lot