File "/home/wakisa/miniconda3/envs/phylophlan/lib/python3.10/site-packages/scipy/spatial/distance.py", line 2555, in num_obs_y raise ValueError("The number of observations cannot be determined on " ValueError: The number of observations cannot be dete

Microbial community profiling PhyloPhlAn
1

Hi,
I am getting this error when I try to draw a heatmap using: phylophlan_draw_metagenomic -i <output_metagenomic> --map <bin2meta.tsv>

Does anyone know I can fix this please?

2

Hi @Wakisa, thanks for reporting this. Can you please share some data so that I can try reproduce this error?
Also, it would be good if you can point out (i) the version of phylophlan_draw_metagenomic you’re using and (ii) of the scipy package.

Many thanks,
Francesco

3

Dear Francesco,
Thanks. Find the attached compressed file and the layout of the mapping
file I used attached.
I am using version 3.0.36 of phylophlan_draw_metagenomic and 1.8.1 scipy
package.

(Attachment Test_run is missing)

Actino_bins.tsv (2.23 KB)

4

Thanks for the details. I have the same versions as you have, so that shouldn’t be the problem. Have you checked that the files you’re providing contain the correct information? I believe the file you attached in your previous message is the one to specify with the --map param, but without the other table, I can test this further.

Many thanks,
Francesco