Running example files

[JuliaIs]

When I try to run the example files as described in the gubbins manual, I get the message "failed while building the tree". Might anyone know how to fix it?
Thanks!

[andrewjpage]

Hi, Which installation method from https://github.com/sanger-pathogens/gubbins/blob/master/INSTALL.md did you use?

[JuliaIs]

Thanks for the fast answer. I installed it via Bioconda (OSX)

[andrewjpage]

Which version of OSX?

[JuliaIs]

10.8.5

[andrewjpage]

I ran the steps from scratch on my laptop which is running OS X El Capitan (10.11.6), and listed them below. I'm afraid I don't have access to any machines running your version of OSX as it hasn't been used in a number of years here, so cannot test how bioconda works on it. I suspect the age of your OSX is the problem. Your best bet is probably to use the Docker container.

Go to https://conda.io/miniconda.html
Download https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
On the commandline run:

bash Miniconda3-latest-MacOSX-x86_64.sh

Close terminal and open a new one then run:

conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install gubbins

Download ftp://ftp.sanger.ac.uk/pub/project/pathogens/gubbins/PMEN1.aln.gz
Run:

gunzip PMEN1.aln.gz
run_gubbins.py PMEN1.aln

[JuliaIs]

I tried as you described, still the output is "/bin/sh: line 1: 1336 Illegal instruction: 4 raxmlHPC-AVX2 -f d -p 1 -m GTRCAT -V -s PMEN1.aln.phylip -n PMEN1.iteration_1 > /dev/null 2>&1
Failed while building the tree."
I will try to update the OS X to fix the problem. Thank you a lot

[andrewjpage]

The error you posted indicates that your CPU doesn't support the optimisations used by bioconda (AVX2 is only on new CPUs) for raxml. If you manually install raxml and use the AVX or SSE3 versions it should run fine. Regards, Andrew

…

On 1 February 2018 at 10:49, JuliaIs ***@***.***> wrote: I tried as you described, still the output is "/bin/sh: line 1: 1336 Illegal instruction: 4 raxmlHPC-AVX2 -f d -p 1 -m GTRCAT -V -s PMEN1.aln.phylip -n PMEN1.iteration_1 > /dev/null 2>&1 Failed while building the tree." I will try to update the OS X to fix the problem. Thank you a lot — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#211 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABeV13dfLhxxQWz-ZZNblQXwhMZ0xgzks5tQZa6gaJpZM4R1RF6> .