Closed glarue closed 1 year ago
Hello @glarue!
Thanks for pointing this out, I completely forgot to upload the file. You can find it here. Note that I had to use lrzip
for file compression due to size restrictions in GitHub (files should be < 25MB), so you will need to install lrzip
to uncompress the file before feeding it to GenEra.
Regarding the memory problem with ncbitax2lin
, I cannot modify the source code of fmt.py
, but we can open an issue so the owner of the repository can implement this modification.
@josuebarrera thanks!
I mentioned the modification to ncbitax2lin
mostly in the hopes it might help someone else with a quick fix. Ideally, a full PR for that repo would involve propagating that option to the command line arguments for ncbitax2lin
, which isn't something I was inclined to add myself although it would be trivial enough to do so.
Hi @josuebarrera,
Two things:
ncbitax2lin
, but I can't seem to find the link/file itself. Have I overlooked something?ncbitax2lin
memory usage issue by modifying thefmt.py
file fromncbitax2lin
to reduce the number of workers in the call toconcurrent.futures.ProcessPoolExecutor()
(which defaults to the number of CPUs on the system) by addingmax_workers=<n>
, where<n>
is some lower number e.g.,