Lili Andersson-Li

Did an error occur when you ran it with 72GB? I would suggest increasing it to more than 80GB if this process requires more than 72GB.

The same error happened to me by using the **standard krakenuniq database** and `--preload-size 500M`. But the error disappears when using a 20 times smaller database.   So I suspect that...

@jfy133 I have run the tests for the `test`, `test_full`, and `test_krakenuniq`, and all of them passed. Great job! I think we can merge this PR once all tests pass.

It seems that `Pychopper` supports ONT long-read sequencing, whereas `chopper` is compatible with both PacBio and ONT sequences. Therefore, it might be more advantageous to utilize `chopper` in this context.

So I am going to add `porechop_abi` to taxprofiler now as an alternative tool for adapter trimming of long reads

> ### Description of feature > I don't have a lot of experience with all the tools so I can only speak for kraken2 and Bracken: > > ### kraken2...

> I agree that --minlength = 15 is too short. A value of around 30-35 could be a good consideration. It was set to 50 for Illumina data in nf-core/viralrecon....

I apologize for any confusion. In your previous comments, you mentioned the parameter shortread_qc_minlength = 15, which is used in both Fastp and AdapterRemoval to specify the minimum length of...

It's interesting to see the various reference genome options available in HOSTILE, such as combining the `human T2T` genome with `HLA, argos985 and mycob140`. This combination can filter out human...

@jfy133 I agree with you. In our clinical cases, it's quite often to see that false positives caused by human rRNA. Therefore I am considering to include human rRNA databases...