"Warnings" in Pangenome tree (core genes) and error with dplyr and tibble

[Panchastico]

Hi, good day. i have the following problems but my tormes format is generated but with errors.

error reported on command line
"WARNING: Core gene alignment tree was not generated during pangenome analysis. Please check."

and this errors.

i think that this error will be solucionated with the activate
--embed-resources --standalone
but I don't know how to do it, I think the base pipeline commands don't allow it.

the last error

[nmquijada]

Hi @Panchastico

The messages you are receiving in the terminal are "warnings" and not "errors". The --self-contained seems to be now deprecated in rmarkdown/pandoc and other options are recommended, but those things are not causing your tree to fail. We will take care of those changes in the next version, so those warnings do not appear in the report (such as in your last image).

The message "WARNING: Core gene alignment tree was not generated during pangenome analysis. Please check." that you are receiving is automatically displayed by TORMES when it does not find the corresponding newick file and thus the tree cannot be generated.
Could you please check that this file was generated for you? pangenome/core_gene_alignment.newick

Best,
Narciso

[Panchastico]

thank you so much and the file pangenome/core_gene_alignment.newick was not generated :c
the file is blank

[nmquijada]

Hi @Panchastico
Thanks for the info.
The .newick file is generated with FastTree from an output file of Roary. Just to check where the source of the error came from, could you please check if the file pangenome/core_gene_alignment.aln is also empty?
Thanks!
Narciso

[Panchastico]

sorry for the delay. The file you mention is fine.