mzML parsing error

[CarlaCristinaUranga]

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]

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]

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 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#292 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFK6HCZQKMEZNNB774Z4U43TFJ2STANCNFSM4ZYCQRAQ> .

[hbarsnes]

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]

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

[hbarsnes]

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]

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]

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]

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]

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]

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

[CarlaCristinaUranga]

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