Error when running mafft in roary

[igarrom]

I am using roary and a exception appear several times during the execution:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file 'pan_genome_sequences/rplK.fa.aln': No such file or directory
This happens with some genes. Is this normal or I can not trust my results?
Thank you

[RodriguesJA]

Hi - I am also running into this error.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file 'pan_genome_sequences/group_2010.fa.aln': No such file or directory
STACK: Error::throw

This only occurs when I run the -e to utilize Mafft.
Roary doesn't seem to run any errors with the default settings.
I installed roary using conda installation. I've noticed a similar error here: #241

I've tired to re-run prokka to ensure that my .gff files are not the issue as described in issue 241 - non-unique prefixes. Also - when running Prokka the output does not seem to annotate the [GENUS SPECIES STRAIN]. I'm wondering if this might be that these issues are linked? I've tired using an NCBI referenced gbk file for annotation as well to ensure reliable annotation through prokka.

@igarrom have you found a solution?

[igarrom]

Hi @RodriguesJA
I tried to resolve the issue but I could not. I used the files annotated by Prokka which were fine. I forgot to mention that I try the installation through conda as well and finally I decided to do it out of conda, but anyway it should be a way to solve the problem in conda but I do not know. Maybe someone else can help.
It was helpful to me to follow the following instructions:
https://bioinformaticsreview.com/20190309/installing-roary-and-prokka-on-ubuntu/

[RodriguesJA]

Thanks for the reply. I tired a lot of different things, including updating my perl modules, as well as reinstall roary. What ended up working for me was moving all of my files and output directory into the environment that roary was running in. I was trying to use local folders while trying to run roary in a linux environment. Are you using a virtual box or windows subsystem for linux? If you haven't done so update your perl modules and move all of your files into the linux environment and ensure that your output directory is also in the environment. This worked really well for me. Good luck.

[thkuo]

I also encountered a similar issue and finally--after some hours--solved it by reinstalling bedtools. The command that helped me was roary -a, with which I learned the statuses of dependencies.