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kevinkovalchik / RawTools

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.
Apache License 2.0
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System.MissingMethodException: Method 'Array.Empty' not found. #26

Closed sorenwacker closed 5 years ago

sorenwacker commented 5 years ago

Describe the bug I have MS2 data from a bacterial sample. I wanted to generate peaklists from it for further analysis. I can create the raw_Matrix.txt files. Though no mgf files are generated.

I tried a minimal command an ran RawTools parse -f 1_A.raw -m and got the following output:

Processing: 1_A.raw

Indexing linked scan events: 100%

Unhandled Exception: System.MissingMethodException: Method 'Array.Empty' not found. at RawTools.Program.DoStuff (RawTools.ArgumentParser.ParseOptions opts) <0x41315410 + 0x00f7f> in :0 at RawTools.Program+<>c.

b__0_0 (RawTools.ArgumentParser.ParseOptions opts) <0x413153e0 + 0x00013> in :0 at CommandLine.ParserResultExtensions.WithParsed[T] (CommandLine.ParserResult1 result, System.Action1 action) <0x413152c0 + 0x000d2> in :0 at RawTools.Program.Main (System.String[] args) <0x412a1f70 + 0x00337> in :0 [ERROR] FATAL UNHANDLED EXCEPTION: System.MissingMethodException: Method 'Array.Empty' not found. at RawTools.Program.DoStuff (RawTools.ArgumentParser.ParseOptions opts) <0x41315410 + 0x00f7f> in :0 at RawTools.Program+<>c.
b__0_0 (RawTools.ArgumentParser.ParseOptions opts) <0x413153e0 + 0x00013> in :0 at CommandLine.ParserResultExtensions.WithParsed[T] (CommandLine.ParserResult1 result, System.Action1 action) <0x413152c0 + 0x000d2> in :0 at RawTools.Program.Main (System.String[] args) <0x412a1f70 + 0x00337> in :0

Description of raw file It is MS2 data from an Orbitrap. The file is ~2GB in size.

kevinkovalchik commented 5 years ago

So this happens when you use RawTools parse -f 1_A.raw -m but not when you use RawTools parse -f 1_A.raw -p? Which version of RawTools are you using?

kevinkovalchik commented 5 years ago

Also, does this happen for all your raw files or just this one?

sorenwacker commented 5 years ago

Apparently, this was an error related to mono. I installed version 5.14.0.177. Now, the mgf files are generated. With RawTools parse -f file.raw -m.

kevinkovalchik commented 5 years ago

Okay. Thanks for letting us know!

On Mon, Jan 28, 2019, 4:47 PM Sören <notifications@github.com wrote:

Closed #26 https://github.com/kevinkovalchik/RawTools/issues/26.

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