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mzML parsing error #292

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CarlaCristinaUranga opened this issue Mar 24, 2021 · 11 comments
Closed

mzML parsing error #292

CarlaCristinaUranga opened this issue Mar 24, 2021 · 11 comments
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@CarlaCristinaUranga
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Hi, any idea as to why I am getting this error (please see attached)? The error occurred when parsing the mzML file. I am using SearchGUI 4.0.22 CLI.

Thanks!

Carla Uranga

SearchGUI.log

sal6_rep1.log

@hbarsnes hbarsnes self-assigned this Mar 24, 2021
@hbarsnes
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Hi Carla,

There seems to be an error when parsing the mzML file: "An invalid XML character (Unicode: 0x0) was found in the element content of the document."

Could it be that the mzML contains non-standard characters? Where did the file come from?

If you can share the file I can always take a closer look.

Best regards,
Harald

@CarlaCristinaUranga
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CarlaCristinaUranga commented Mar 25, 2021 via email

@hbarsnes
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Please see attached.

Seems like the attachement was lost along the way. You need to upload it via the issues page. Attaching it to the email does not work. I also have trouble downloading the mzml file you sent me. For some reason I only get a preview but no download option...

Best regards,
Harald

@hbarsnes
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Never mind the issues with downloading the mzml file. I figured it out. :)

@hbarsnes
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Hi again. I have no problems parsing the mzml file you sent me. Are you sure it's the same as the one where you have the issue above?

@CarlaCristinaUranga
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So on the server it seems to be an issue with MS-GF+, which does not complete processing and does not produce an output file. I am able to run it on my desktop with a smaller database (to test), so it should run on the CLI, but for some reason it is not. Thank you so much Harald!

Carla

sal_7.log
SearchGUI.log

@hbarsnes
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Seems to be an issue with the size of the database: #293

Can you try increasing the amount of memory given to SearchGUI (and as a consequence to MS-GF+)?

Or simply skip MS-GF+. :)

@CarlaCristinaUranga
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So I tried a really small database and am still having issues with msgf on the CLI:

rev_human.fasta
SearchGUI.log
sal_7.log

@CarlaCristinaUranga
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sal_7.log
SearchGUI.log

I am not sure it is a database size issue. Thank you kindly for your attention to this!

Kind regards,

Carla

@hbarsnes
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From the SearchGUI log file it seems like you are trying to run Andromeda? However, Andromeda is not support on Linux.

@CarlaCristinaUranga
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Hi Harald you were right, it was a database size issue. I am now working with a 1 GB database and it is working. Thank you so much! It is great to know what we can and cannot do with SearchGUI.
Best wishes,
Carla

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