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mzML parsing error #292
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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, |
Ok so something is happening now, but the results are not generated. Please
see attached.
Best,
Carla
…On Wed, Mar 24, 2021 at 4:45 PM Harald Barsnes ***@***.***> wrote:
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
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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, |
Never mind the issues with downloading the mzml file. I figured it out. :) |
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? |
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 |
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+. :) |
So I tried a really small database and am still having issues with msgf on the CLI: rev_human.fasta |
I am not sure it is a database size issue. Thank you kindly for your attention to this! Kind regards, Carla |
From the SearchGUI log file it seems like you are trying to run Andromeda? However, Andromeda is not support on Linux. |
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. |
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
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