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Hello Jonathan, this is Jack, the person you contacted at UF HPG about the issue. I will document here what I did to fix this for anyone else.
The DALIGNER provided by the bioconda channel through conda is old and does not have the -P option, therefore I had to pull their git repo, compile the code, and then place it into the Strainline env.
I created a PR in the bioconda repo to update the version provided by bioconda which would make installing Strainline easier and true to the install guide here.
Hello,
When running Strainline I am getting an error that says
HPC.daligner: -P is an illegal option
.When I run
HPC.daligner
the output I get is:This error is leading to this error:
PosixFdInput(reads.*las,0): No such file or directory
I hope this is a simple mistake or an easy fix.
Cheers,
Johnny
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