Daniel Straub

I would close that issue as "not planned" because there doesnt seem to sufficient interest. Please re-open in case 454 analysis is wanted and someone actually wants to tackle it.

Hi there, yes that is an interesting database indeed. I dislike however that its very much centered on QIIME2 and the V4-region. GTDB also allows harmonizing between 16S and shotgun...

Greengenes2 support is now for QIIME2 available in the dev branch and will be in the next release. I dont close that issue though because there is still no news...

Hi @aimirza , it seems that `greengenes2` is an option for `--qiime_ref_taxonomy` as in https://nf-co.re/ampliseq/2.11.0/parameters/#qiime_ref_taxonomy... where would you expect to appear "greengenes2" as option where it doesnt?

> How are you using qiime2 to classify ASVs with the greengenes2 database? The following files are used https://github.com/nf-core/ampliseq/blob/0473e157ac9a7b1d36845ff9f8fa7ac843d3b234/conf/ref_databases.config#L373-L378 to extract sequences with primers and train the classifier.

> QIIME2_EXTRACT is running 8h 58m on our hpc yes, I tested it and it takes long, check out https://github.com/nf-core/ampliseq/pull/666#issuecomment-1888609190 It was implemented that way because it caters to every...

What about the cpus and memory, are they altered successfully? If yes, check your `--max_time` setting, maybe another config is overwriting it?

Hi there, this is going way out of the scope of this issue (adding gg2 database). Your problems are not related to gg2, but to executing a large job on...

Thanks for detailing the solution! Did you figure out whether `singularity runOptions` was needed in addition to all the `TMP` and `CACHEDIR` settings, or just the latter?

I actually face the exact same issue. Modifying the gtf to have to each gene_id also a gene_name replaces the "unselected rows" with the usual annotation and adds colors. Labels...