Re: [iqtree] slurm_script: line 52: iqtree: command not found

[Heiko Schmidt]

Dear Deepti,

This is not actually an error caused by iqtree.

It means that the iqtree executable ist not in any directory that is listed in the PATH variable.

It can be solved by either (a) copying the iqtree executable into one of the paths listed in the PATH, or (b) extending the PATH variable by a path that contains the iqtree executable, or (c) use the full path to where your executable is located like

/whereever/this/is/bin/iqtree -s clean.full.aln -m MFP+ASC -B 1000

or

./iqtree -s clean.full.aln -m MFP+ASC -B 1000

if it is in the same directory.


One more reason comes to my mind - if the SLURM is setup such that you are starting in a different directory that the one you submit the job, this can also cause problems.

In any case, you should contact your local system/IT admins (or experienced colleagues), because they are the ones who should be able to tell you. I can only guess, because I cannot know your setup.

Best wishes,
Heiko



> On 24.08.2021, at 07:51, deepti r <deepti....@gmail.com> wrote:
>
> Hi,
>
> I'm new to bioinformatics and have a error when I'm trying to run iqtree. The error message is : slurm_script: line 52: iqtree: command not found
>
> The script I'm trying to run is: iqtree -s clean.full.aln -m MFP+ASC -B 1000
>
> Thank you,
> Deepti
>
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Heiko Schmidt
Center for Integrative Bioinformatics Vienna (CIBIV)
University of Vienna / Max Perutz Labs
http://www.cibiv.at/
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