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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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Unhandled exception in SearchGUI-4.0.0-beta #411

Closed VladimirRoudko closed 4 years ago

VladimirRoudko commented 4 years ago

Hello,

I was running into issue with MS Amanda search within SearchGUI-4.0.0-beta pipeline. The search result in STDOUT the following error:

Unhandled Exception: System.TypeLoadException: Could not load type 'MSAmanda.CommandLine.MSAmandaSearch' from assembly 'MSAmanda, Version=2.0.0.14665, Culture=neutral, PublicKeyToken=null'.

Eventually, no output file is produced. My machine configurations are: Ubuntu Java openjdk 11.0.7 2020-04-14 Xmx40G Threads 15

Thank you! Vladimir

VladimirRoudko commented 4 years ago

According to what I've been able to find out, the error is happening upon commandline trying to load MSAmanda.exe file with mono:

"mono /path/to/SearchGUI-4.0.0-beta/resources/MS Amanda/MSAmanda.exe -s ..."

Apparently, similar commandline was working using SearchGUI-3.3.20 version (with MS Amanda Stand-Alone version 2.0.0.9706). Is it possible, that update to version 2.0.0.14665 has affected the ways how mono operates?

Thank you, Vladimir

hbarsnes commented 4 years ago

Hi Vladimir,

As far as I know there are no changes in how mono operates for the different MS Amanda versions. Do you get the same error if running the MS Amanda mono command line directly, i.e. not via SearchGUI? If so, I'd recommend contacting the MS Amanda developers directly at https://groups.google.com/forum/#!forum/msamanda.

Best regards, Harald

VladimirRoudko commented 4 years ago

Hi Harald,

yes, indeed I get the same error directly running mono with MSAmanda.exe. I will post the error on the forum - thank you for the link!

Vladimir

VladimirRoudko commented 4 years ago

Turned out to be mono-compatibility issue on Linux platform. The error is fixed by changing mono runtime to mono complete, explanation is here:

https://groups.google.com/forum/#!msg/msamanda/XRKS2yYA2Jw/R9rFPEFOBAAJ

Again, thanks for help!