And this warning message:
In addition: Warning message:
In .getcdsIDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type stop_codon. This information was
Salmon version: 1.2.1
Tximeta version: v1.6.2
Newest R and RStudio versions.
Normally i would ignore the warning, but the error does not permit me to continue. I believe, that the website is not working. Has it moved to a different domain or just temporary unavailable?
This hasn't happened before, but it affects core packages upstream, so either it will be resolved on the UCSC side (maybe it's just down right now) or on the Bioc side (maybe they moved the location and we need to update).
In the meantime, you can use skipMeta=TRUE to import the transcript-level counts. Maybe I can work on a work-around in the case that this is the only metadata task that is broken (but e.g. the GTF file is reachable, parsed, cached locally, etc.)
The download server seems to be down. But do note that tximeta is simply downloading a freely available resource, which is different from being responsible for that resource, or for that matter knowing anything about what the suppliers of that resource might be up to. That sort of question should be directed to the folks at UCSC Genome Browser.