[BUG] - mzML file import error

[Sjors455]

Bug description
When I try to import a file (converted from RAW to mzML using MSconvert following this video https://www.youtube.com/watch?v=xnjvZlSlp40) I get the same error message every time, see attached screenshot. This also happens after starting a new project and re-installing. The file consists of LC-HRMS data including full scan, DIA and DDA spectra and was recorded on a orbitrap.

Expected behavior
I expect the file to be imported for further processing.

Steps To Reproduce
Open sirius
Click import in the top-bar
Select file using file browser (i have it on the C-drive)
Wait for it to process, progress bar does things
Error (see screenshot)

Screenshots and Log Files
Copy:

Data import failed. This project may be incomplete or corrupted.
We recommend discontinuing its use.

java.lang.Exception: java.lang.ArrayIndexOutOfBoundsException

java.lang.Exception: java.lang.ArrayIndexOutOfBoundsException at io.sirius.ms.sdk.jjobs.SseProgressJJob.updateAndCheckIfDone(SseProgressJJob.java:128) at io.sirius.ms.sdk.jjobs.SseProgressJJob$1.onNext(SseProgressJJob.java:75) at io.sirius.ms.sdk.jjobs.SseProgressJJob$1.onNext(SseProgressJJob.java:64) at io.sirius.ms.sse.FluxToFlowBroadcast.lambda$onNext$7(FluxToFlowBroadcast.java:103) at java.base/java.lang.Iterable.forEach(Unknown Source) at io.sirius.ms.sse.FluxToFlowBroadcast.onNext(FluxToFlowBroadcast.java:99) at io.sirius.ms.sdk.SiriusClient.lambda$enableEventListening$3(SiriusClient.java:201) at reactor.core.publisher.LambdaSubscriber.onNext(LambdaSubscriber.java:160) at reactor.core.publisher.FluxPublishOn$PublishOnSubscriber.runAsync(FluxPublishOn.java:446) at reactor.core.publisher.FluxPublishOn$PublishOnSubscriber.run(FluxPublishOn.java:533) at reactor.core.scheduler.WorkerTask.call(WorkerTask.java:84) at reactor.core.scheduler.WorkerTask.call(WorkerTask.java:37) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source)

Example data

Include any additional information that might help the development team to reproduce the bug, in particular relevant project files or datasets, that demonstrate the problem you are reporting.

System Info (please complete the following information):

• OS and Version: Windows 10 enterprise
• SIRIUS Version 6.1.1

[MartinHoffmannJena]

Hi,

I'm assuming this happens because your file contains both DDA and DIA data. SIRIUS expects an .mzML file to contain one run, are these fullscan, DDA and DIA measurements taken from multiple runs and somehow merged?

[Sjors455]

Hi,
Thanks for your reply. The data is from 1 run, we just have all the different scan "events" included in a scan (so full scan, DDA top 4, then DIA separated in a few windows). So nothing has been merged and the data is from 1 injection.