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]