Sam Lambrechts

snakemake does not find mamba or conda

7

When I run` snakemake --use-conda -k -j 8` I get: `Error: mamba package manager is not available. ..... ` and when I run `snakemake --use-conda -k -j 8 --conda-frontend conda`...

Custom database

7

Hi, On the main github page it says DRAM can also use custom user databases. Is it explained somewhere how to do this? I have fasta files containing protein sequences...

Hi, I see that minimum bitScore of a search to retain hits is 60 by default. I am working with custom databases and I notice in the `annotations.tsv` file that...

Error in rule binRefine (one of the commands exited with non-zero exit code)

11

Hi Francisco, When running `bash metaGEM.sh -t binRefine --local` with the metagem env activated, I seem to get a "`(one of the commands exited with non-zero exit code; note that...

No metabat/samplename/cov/*.all.depth file and an empty concoct coverage_table.tsv

1

Hi Francisco, For 4 out of 43 samples, the `/metabat/samplename/cov/*.all.depth` files are missing, the concoct `coverage_table.tsv` file is empty, but the `/maxbin/samplename/cov` folder does contain depth files. Does that mean...

Cannot install SWISS::Entry; and SWISS::KW; perl modules

1

Hello, When I try to install the required SWISS::Entry; and SWISS::KW; perl modules using cpan, I get: ``` (base) slambrecht@WE11sv03:~/.local/share/.cpan/build/local-lib-2.000024-oG3DdT$ cpan SWISS::KW; Loading internal null logger. Install Log::Log4perl for logging...

Consequences of using vsearch on NovaSeq data

3

Hi, I know there are consequences of using dada2 on NovaSeq data (e.g. https://github.com/benjjneb/dada2/issues/791), but do you know if there are similar problems with using vsearch on novaseq data? Best,...

Hi, When using the phyloseq shiny `shiny::runGitHub("shiny-phyloseq","joey711")` I get the following error message when trying to download the compressed file containing the code and data necessary to reproduce the analysis...

Dear GTDB_Kraken, First off, thank you for sharing this! I was wondering whether the taxonomy folder you included is compatible with the standard reference libraries provided by kraken2-build? In other...

Pavian with amplicon sequencing data

1

Hi, Is there a way to use Pavian with amplicon sequencing data (e.g. 16S or 18S)? Best, Sam