Sean

Probably obvious to everyone but, as a workaround, you can download from: https://zenodo.org/records/5571251 , unpack and set the location manually ``` checkm2 database --setdblocation your_database_path/CheckM2_database/uniref100.KO.1.dmnd ```

After looking at my input files and the extract_kraken_reads.py code I figured out this issue. My preprocessing code failed to append the /1 and /2 tokens to the read names...

I'm not conversant in nextflow/singularity, but this might be relevant: https://github.com/bioconda/bioconda-recipes/issues/11583

I'm having the same issue. RStudio (R version 3.5.0 (2018-04-23)) > pavian::runApp(port=5000) Loading required package: shiny Warning: package ‘shiny’ was built under R version 3.5.2 Loading required package: pavian Attaching...

Just a little bit of clarification, this only seems to happen with the human download: ``` 09:39 cn0628 20200211_standard+_kraken2$ kraken2-build --download-library human --db ./ mv: try to overwrite 'assembly_summary.txt', overriding...

Actually, the fix here is easy (I think). download_genomic_library.sh just needs to be modified to deal with the move command trying to clobber the assembly_summary.txt file. Current code: ``` if...