Trying to build a West Nile Virus Tree but failing at the rule tree step

[saj]

Hi Nextstrain! I am trying to build a west nile virus tree but it’s failing at my rule tree step. I git cloned GitHub - grubaughlab/WNV-nextstrain: the repository used to build West Nile Virus for nextstrain and using the repository as a guide for my new build. My input data is the data from this repository, my sequencing data and new WNV sequences. Here is the error message I get :

I tried looking at the log file, it seems to have duplicated sequences from the dataset, but it still ran. I think my run failed on this command: raxmlHPC-PTHREADS-AVX -T 2 -f d -m GTRCAT -c 25 -p 235813 -n b260ff -s results/aligned.fasta > RAxML_log.b260ff

Any input will be awesome. Thanks in advance.

[james]

Hi @saj – can you try setting the environment variable NCBI_EMAIL so that the first error can be fixed? I’m not sure if that’ll solve the tree building error, but it may do.

[saj]

Thanks, yeah I tried setting the NCBI_Email variable, it progressed further but errored out at the build tree step. Looking at the top error it seems like my Python might not be configured for Tk, will try to resolve that and troubleshoot again.

[trs]

@saj Take a look at matplotlib’s documentation on “backends”, which talks about how to resolve the Tk issue. If you want to avoid messing with Tk, you can probably change this line in scripts/make_colors.py:

mpl.use('TkAgg')

to

mpl.use('Agg')