Error with Biom format output from kraken2 report

taxprofiler / taxpasta

TAXnomic Profile Aggregation and STAndardisation

https://taxpasta.readthedocs.io/

Apache License 2.0

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Error with Biom format output from kraken2 report #144

Closed UmaJan closed 6 months ago

UmaJan commented 8 months ago

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Question

[Question] I am having trouble with creating a biom output from a kraken2 file despite using pip install instructions as given in the readme. I have also made sure to use a pyenv 3.11.7 as that is one of the versiosn that is supported by biomformat. I have attached the error message below

jfy133 commented 8 months ago

I think this is because only taxpasta merge supports BIOM... @Midnighter is there a reason why no BIOM for standardise? Does it only support multipl samples, for example?

Midnighter commented 8 months ago

Yes, BIOM was intended as a format for groups of samples. That is why it's currently not implemented for standardize. Also see https://github.com/taxprofiler/taxpasta/issues/138#issuecomment-1741719063

jfy133 commented 8 months ago

Ok, I guess then close as not planned? I also agree with the comment it doesn't make much sense...

Midnighter commented 8 months ago

Unless there is an overwhelming desire for having this, I would close it yeah. Although, it's coming up enough that we might want to put it in FAQ or similar?