Maxime Borry

It's a nice to have TAXID entry to report sequences that couldn't be attributed to any reference :) Thanks @nick-youngblut and @shenwei356 , I'll have a look at https://github.com/shenwei356/gtdb-taxdump when...

Just a comment to upvote this feature request, it would make make Pandera super nice to use for https://github.com/spaAM-community/ancientmetagenomedir/tree/dev and https://github.com/SPAAM-community/AMDirT

That's what was missing, great that it is coming to the GH actions !

Checkm2 is (kind of) out ([preprint](https://www.biorxiv.org/content/10.1101/2022.07.11.499243v1), [repo](https://github.com/chklovski/CheckM2)), and from a brief look at the code, it looks that they reproduced the same mistake with singularity. But it's been caught early...

The other problem with competitive mapping comes later when you want to do some variant calling: because multi mapping read get a very low MAPQ score, they are typically ignored...

I'm running into the same problem on a cluster when using remote execution. Running the process on a local node, even using singularity works fine for me.

I'm unfortunately getting the same error message :( Also side note, since the species _Lactobacillus plantarum_ has been renamed in _Lactiplantibacillus plantarum_ I unfortunately have to used an outdated species...

Newer versions of GTDB-Tk require significantly less memory than the one currently available in mag. See https://github.com/Ecogenomics/GTDBTk#new-features > This reduces the memory requirements of GTDB-Tk from 320 GB of RAM...

@lh3 Same problem here, with a SAM output on simulated Illumina data. However if I don't use the `--split-prefix` flag, it works. ## Example: ```bash $ minimap2 -d index.mmi genomes/Agrobacterium_tumefaciens.fa...

Also tagging @hasindu2008