HPC.daligner option issue

[jonathan-bravo]

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:

Usage: HPC.daligner [-vbad] [-t<int>] [-w<int(6)>] [-l<int(1000)>] [-s<int(100)]
                            [-M<int>] [-B<int(4)>] [-D<int( 250)>] [-T<int(4)>] [-f<name>]
                          ( [-k<int(14)>] [-h<int(35)>] [-e<double(.70)>] [-H<int>]
                            [-k<int(20)>] [-h<int(50)>] [-e<double(.85)>] <ref:db|dam> )
                            [-m<track>]+ <reads:db|dam> [<first:int>[-<last:int>]]

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

[jaeakle]

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.

https://github.com/bioconda/bioconda-recipes/pull/43162

[jonathan-bravo]

Thank you Jack,

I will leave this issue open for now so it is easier to find.

Once the pull request has been accepted I think it will be appropriate to close the issue then.