Stephen Turner

I'm running into the same problem. My gcc is 4.8.5. Not working via bioconda either.

Awesome. I will try this out soon. cc @punkrockscience, give it a try?

i've also just `brew install nullarbor --HEAD` and `brew install prokka --HEAD` and still get the same issues. it looks like prokka is using the --compliant option. in the Makefile...

This hack seems to help. With the nullarbor Makefile: ``` sed -i 's/locustag SRR[0-9]*/locustag x/g' Makefile ```

We've been doing this externally using some R code to traverse phylotree, which was put into a JSON structure using some python code Pete found. We'll try to clean this...

FWIW, I've seen this a couple of times as well, running the CLI version.

Thanks Sebastian! We were using a VCF file at the time. Unfortunately it's a sample that can't leave the building, but I'll see if we can test 2.2.6 on that...

see also #9

It does. I think you'll have to use an archived version, e.g., https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html#using-archived-versions-of-ensembl On Thu, Aug 30, 2018 at 4:12 PM John Thompson wrote: > If I want to update...

So I'm looking at the code and it's the `ensembl_version` object that's created during the build process that's recording the actual version. ```r ensembl_version % filter(biomart == "ENSEMBL_MART_ENSEMBL") %>% pull(version)...