Help with FileFilter node configuration

#1

Hi all,

I am new in Knime/OpenMS, and I am trying to use the software GlycopeptideGraphMS, that requires a preprocessing data inside Knime. I got the workflow from the page of the software, but when I try the run it, I got an error in the FileFilter node.

The message is :

ERROR FileFilter 3:53 Failing process stdout: [Progress of ‘loading spectra list’:, , 4.11 % , 36.99 % , 73.97 % , 83.22 % , 87.84 % , 92.46 % Error: Unable to read file (- due to that error of type Parse Error in: C:\jenkins\ws\openms_release_packaging\c2e226b2\source\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp@105-void __cdecl OpenMS::Internal::XMLHandler::fatalError(enum OpenMS::Internal::XMLHandler::ActionMode,const class OpenMS::String &,unsigned int,unsigned int) const)]
ERROR FileFilter 3:53 Failing process stderr: [C:\jenkins\ws\openms_release_packaging\c2e226b2\source\src\openms\source\FORMAT\HANDLERS\XMLHandler.cpp(104): While loading ‘C:\Users\Debora\Documents\DRAFT_PhD\Teste GlycopeptideGraphMS\QEHF1_9628_DAS.mzML’: input ended before all started tags were ended; last tag started is ‘binary’( in line 86365 column 95259)]
ERROR FileFilter 3:53 Execute failed: Failed to execute node FileFilter

I think the problem is in the configuration of the OpenMS plugin inside Knime, but I do not know how to fix it. Please, may someone know how to fix it?

Thank you very much,

Best regards,
Debora

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#2

Hi Debora,

welcome to KNIME Community Forum.

I have moved your topic to OpenMS category. Hope you will get help soon :wink:

Br,
Ivan

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#3

Hi Debora,

this sounds like a corrupted file. Can you maybe redownload or try with other input mzMLs first?
And is it the first node in the workflow?

Best,
Julianus

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#4

Hi Ivan,

Thank you so much for your help!

Best regards
Debora

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#5

Hi Julianus,

Yes, I can do it.
No, it is a large workflow created by Glycopeptide GraphMS developers, and the FileFilter node is in the middle of the workflow, after an input file node.

Thank you so much for your help,

Best regards,
Debora

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#6

Hi Julianus,

Just to let you know that you were right.
I changed the file and now the workflow works perfectly.

Thanks again!

Best regards,

Debora

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