Qiyun Zhu

I think a few commands (like Qiita does on SHOGUN) or a workflow manager (like Oecophylla does on SHOGUN) both work. Although in some use cases, especially when the input...

@wasade Thanks for explaining the challenges and risks of doing parallel compute! Much of it is beyond my current knownledge but it is good learning experience to me. The parallel...

Hi @wasade Thanks for explaining to me the knowledge! I just had time to seriously learn Python profiling after this long while. Made some progress, and working on bottlenecking steps...

@mortonjt @antgonza I do think this is an important feature to have. So far Woltka doesn't have parallelization built-in. I work-around (probably similar to what Antonio used) is to run...

I currently do not have a good idea. Working with those large files is naturally hard. One cannot be very certain of the file format unless they read the entire...

Hello @raplayer Thanks for reporting this issue. I believe that you have figured out that Centrifuge raw output is not currently supported as an alignment file format for Woltka. Actually,...

@rgommers Fantastic! It worked. Thanks for the instruction!

@wasade It will be very nice if this can also be resolved prior to the new release. You are probably the most familiar with the issue. But if necessary, I...

@wasade I tried to pip install biom-format 2.1.16 along with numpy 2.0rc1 but it ran into issues. Procedures to reproduce: ```bash > conda create -y -n biom-np2 -c conda-forge python...

I guess once NumPy 2.0 is officially released, the current package (biom-format) will automatically build against 2.0 when it is being installed, so there is nothing we need to do...