Hello! I am trying to use the “ARTIC minion” tool on galaxy and even though I select different version of the ARTIC primers (from the drop down menu or bed files I upload) it still uses the V1 (when I open the log file is says that it uses V1 scheme). Can anyone tell me what can be the problem? Because I get a consensus that has a lot of Ns.
Thanks in advance!
Welcome, @tbzh13
To confirm proper inputs, you could use this shared history resource to compare/replace what you are using now. SARS-CoV-2 ARCTIC V4 files - #3 by wm75
@tbzh13 that log is a bit unfortunate and misleading, but what the tool actually does seems to be the right thing.
I just tested with a primer scheme from one of my histories and the generated command line has this part:
mkdir -p 'scheme/name/V1' && ln -s '/data/dnb-ds02/galaxy_db/files/020/532/dataset_20532843.dat' 'scheme/name/V1/name.scheme.bed'
where '/data/dnb-ds02/galaxy_db/files/020/532/dataset_20532843.dat' is really where my primer scheme file lives on the server.
In other words, the tool merely always links your custom primer scheme into a “scheme/name/V1” folder in the job working directory, from where it gets picked up by the ARTIC minion pipeline, but unfortunately that leads to that confusing log.
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