Ali Mirza

My build process also broke during the masking process for the nt database. Please advise how we can properly continue the masking processes without starting over again.

I wrote a script that solved the problem without starting over. This example uses `library.fna` as the original fasta library and `library.fna.tmp` as the incomplete masked file produces from `kraken2`...

@Maggie8888 Same thing happened to me. The problem is that global test is not working with random effects. I was able to reproduce the error using the codes below using...

These issues might arise because the current implementation of the global test likely assumes a simpler fixed-effect structure. Using packages like `lme4` or `lmerTest` for random effects modeling can potentially...

Another reason for adding a predetermined sampling fraction is related to how we prepare our count table for ANCOM-BC analysis. Often, we pre-filter this table, removing ASVs (Amplicon Sequence Variants)...

**I resolved the issue!** Through simulated data, I discovered that random effect models are incompatible with the ANCOMBC2 global test (see #262 ). Additionally, the global test can fail if...

Hi Daniel. Thank you for the update. I do see greengenes2 in the github page but it doesnt show as one of the parameter options on your nextflow page. Just...

My mistake, I was looking at `--dada_ref_taxonomy` .

> Paper: https://www.nature.com/articles/s41587-023-01845-1 How to use it: https://forum.qiime2.org/t/introducing-greengenes2-2022-10/25291 > How to use it: https://forum.qiime2.org/t/introducing-greengenes2-2022-10/25291 How are you using qiime2 to classify ASVs with the greengenes2 database? Are you following the...

Wow, extracting reads (`QIIME2_EXTRACT`) takes a long time. It ran for a day and got canceled because of the default 1 day limit. I increased the limit and now waiting....