Narciso Martin Quijada

Hi Brad, Thanks for sharing the file. It seems that it run without errors this time, right? For pangenome analysis one of more sample is needed in order to perform...

Hi Brad, Thank you very much for sharing the solution! It will be very helpful for other users encountering the same issues. I will include this actions in the ```tormes-setup```...

Hi @aartdvark Could you please re-run your analysis by redirecting the screen output/errors to a file and then share that file with me? You can do it like this: https://github.com/nmquijada/tormes/issues/6#issuecomment-538347884...

Hi @aartdvark I checked your error file and TORMES didn't quit after Quast, as all the analysis that have to be performed after Quast (annotation, antbiotic resistance and virulence screening,...

Hi @plantman8 @biobrad is correct. How tormes is built right now, there's a bug that it does not accept full but relative paths for the `-o/--output` option. This issue has...

Hi all, Indeed, the problem with Mauve is that conda installs the newer Mauve version (2.4.0.r4736-1) instead the one I used for creating the conda yaml file (2.4.0.r4736-0). The problem...

Hi @shlomobl Thank you for the update! :) I am closing this issue now but feel free to reopen! Best, Narciso

Solved with your new yml file (+ mamba if needed). Hope this solution lasts for some time :)

Hi @ddesai5 Did you try @biobrad solution? Alternatively, you can run TORMES again but by redirecting the output: ``` [YOUR TORMES COMMAND] &>>error-tormes.txt 2>>error-tormes.txt & ``` By doing so, you...

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...