NaN value after distmat in StrainPhlAn

Microbial community profiling StrainPhlAn
1

Hello developers,

I am running the StrainPhlAn referring latest tutorial, and encountering some problems.
I ran through the instructions and reached the step of producing an ordination plot.
When I ran distmat by a code:

distmat -sequence strainphlan_output/t__SGB17248.StrainPhlAn4_concatenated.aln -nucmethod 2 -outfile strainphlan_output/t__SGB17248.distmat

I got a output file (~.distmat) whose one of samples had NaN value for all comparsion to other samples. This NaN made an error with running strainphlan_ordination_vis.R at > cmdscale() function.

Some previous forums suggested turning NaN into 0, however, I doubt that it is correct.
Do you have any suggestions or solutions?

Thank you
Best regard, Gihyeon

Tools [version]

  • distmat [EMBOSS:6.6.0.0]
  • strainphlan [4.0.6]
2

Hi @Kim-Gihyeon
The strainphlan_ordination_vis.R script is part of the biobakery workflows, could you please move the post to the subforum: bioBakery workflows - The bioBakery help forum
There they will better assess your issue

3

Thank you for your prompt response!

And, I am sorry about making the topic on the wrong forum.

I just posted the same topic here.

Should I remove this present topic myself or maintain it?

Thank you for your help.
Best regard, Gihyeon.

4

Hi, @aitor.blancomiguez.

I’ve waited for response for a couple of months, but nothing replied.
So, I ended up reminding you of this post. (Actually, the moved post was relocated to StrainPhlAn forum because this error is not from strainphlan_ordination_vis.R)

Basically, I just wonder how to deal with ‘nan’ in the distance matrix from distmat.

Thank you for your help.
Gihyeon