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I am getting this error with MaxQuant 1.6.14 running with mono (5.14.0.177=he1b5a44_1001).

System.IO.FileNotFoundException: Could not find file "/home/ubuntu/run-dir/combined/combinedRunInfo"

And I not sure why I am getting this error. The process has read and write permissions to that location.

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...seems the mqpar file was not compatible with the maxquant version.

Make sure the mqpar.xml file shows the same version number as the MaxQuant binary. MaxQuant is not really made for the command line. So, the errors shown are sometimes quite misleading.

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