failed while running raxml internal sequence reconstruction gubbins

[samlipworth]

I get the following error, the sequences are all of decent quality, I'm running gubbins installed through conda. What is the issue?

[tseemann]

Can you try installing the latest version manually?
The authors have made a bunch of improvements recently: https://github.com/sanger-pathogens/gubbins/releases/tag/v2.3.4

[lexleong]

I also keep getting the same issue with raxml internal sequence reconstruction. I have recently installed the latest version from conda. When you said manually, do you mean via "sudo-apt get" instead?

[DorothyTamYiLing]

Hi,

I was trying to install Gubbins on Amazon web service. For some reason I could not install the latest version 3.3 (or 3.2.1) .I only managed to install version 2.3.4, as suggested by the above post. However I still get the error message:

ubuntu@ip-172-31-45-187:~/gubbins-2.3.4/python/scripts$ run_gubbins.py --version 2.3.4 ubuntu@ip-172-31-45-187:~$ /home/ubuntu/gubbins-2.3.4/python/scripts/run_gubbins.py --prefix biofilm180 --starting_tree 180sample_cg.phylip.treefile 180sample_cg.fasta Failed while running RAxML internal sequence reconstruction

Please I would like to get some help here.

Thanks, Dorothy

[nickjcroucher]

The fix is to install the latest version. I don't know why the most recent version wouldn't install through conda, but that would be a separate issue.