I am trying to run saige and getting this error. Not sure what could be the reason for this. Can you help me out regarding this?

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Comments

3 comments

  • Comment author
    Chai Fungtammasan DNAnexus Team

    The error saying that it can't fine the file. You can run the app in debug mode (e.g. --debug-on All) and ssh into work station to see why such file doesn't exist there.

    In general, could you provide more context when you ask questions? Like is it your custom applet, Swiss-army-knife app, etc. That would be useful for other community member to understand the scenario that you had issue with.

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  • Thank you so much for the response. The issue is that I didn't keep the `in_sparsegrm_kin` parameter as true while running SAIGE but supplied a sparse matrix as input. That's the reason for the issue. I have corrected it. Thank you so much for your help. I will follow the above criteria for reporting in the future.

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  • Comment author
    Chai Fungtammasan DNAnexus Team

    Glad to hear that you figure out the issue!!

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