ERROR! bed file does not exsit

[nm15336]

Hi, I am running step 1 of saige using plink genetic files. However I am getting the error:

Error in fitNULLGLMM(plinkFile = opt$plinkFile, bedFile = opt$bedFile,  :
  Error in fitNULLGLMM(plinkFile = opt$plinkFile, bedFile = opt$bedFile,  :
  ERROR! bed file does not exsit

The data do exist, is in the right dir, and I have tried renaming the files, changing their location, adding and removing "", but get the same error.

Is this because I am calling it through a singularity module? Is there a reason it would not recognise the files?

singularity exec ${saigeDir} step1_fitNULLGLMM.R \

Or do you know what else could be causing this? Full .out file attached. Thanks! saige-error-git.txt

[kscott-1]

In general when working with containers, you will need to mount your data into the container

apptainer exec --bind /path/to/plinkfile:/mnt .......

Then your plink files will all be located in the /mnt directory within your container

I suggest reading through the apptainer docs

[nm15336]

Thank you!