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Error when importing .mzml files #209

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sra34 opened this issue Oct 18, 2024 · 1 comment
Open

Error when importing .mzml files #209

sra34 opened this issue Oct 18, 2024 · 1 comment
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linked to dev Mark if this issue has been linked to an internal development issue. probable bug Marks bug reports where the reported issue has not yet been confirmed/reproduced

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@sra34
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sra34 commented Oct 18, 2024

Bug description
I get the following error message every time when trying to upload .mzml files into SIRIUS (v. 6.0.6):

Error when importing data! Cause: java.lang.Exception: com.fasterxml.jackson.databind.JsonMappingException: Index 0 out of bounds for length 0 (through reference chain: de.unijena.bioinf.ms.persistence.model.core.feature.AlignedFeatures["detectedAdducts"]->de.unijena.bioinf.ms.persistence.model.core.feature.DetectedAdducts["detectedAdductsList"]->java.util.ArrayList[0]->de.unijena.bioinf.ms.persistence.model.core.feature.DetectedAdduct$DetectedAdductBuilder["adduct"])
java.lang.Exception: com.fasterxml.jackson.databind.JsonMappingException: Index 0 out of bounds for length 0 (through reference chain: de.unijena.bioinf.ms.persistence.model.core.feature.AlignedFeatures["detectedAdducts"]->de.unijena.bioinf.ms.persistence.model.core.feature.DetectedAdducts["detectedAdductsList"]->java.util.ArrayList[0]->de.unijena.bioinf.ms.persistence.model.core.feature.DetectedAdduct$DetectedAdductBuilder["adduct"])
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$3(SiriusClient.java:203)
at reactor.core.publisher.LambdaSubscriber.onNext(LambdaSubscriber.java:160)
at reactor.core.publisher.FluxPublishOn$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)

The .mzml files have been centroided in msconvert, with msLevel = 1 and 2 data. These same files were successfully imported in SIRIUS version 5, so I am not sure if there is an issue with my files in the newer version.

Here are some example .mzml files that I have tried to import and which have successfully been imported in version 5:

https://drive.google.com/file/d/1-7CneFejGiep-UMK1zpOntd5H9XERTzr/view?usp=sharing, https://drive.google.com/file/d/1wYCKx-zjwa_Zhd7Dusp_OgeP3CRFnr-2/view?usp=sharing, https://drive.google.com/file/d/1yKJskFTueWF6dihputcRl8STJZdrlreL/view?usp=sharing

I am on macOS (Sequoia; 15.0.1), Intel i7, 16 GB.

Thank you for your help!

@sra34 sra34 added the probable bug Marks bug reports where the reported issue has not yet been confirmed/reproduced label Oct 18, 2024
@MartinHoffmannJena
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Thank you for the detailed report, we are looking at this

@MartinHoffmannJena MartinHoffmannJena added the linked to dev Mark if this issue has been linked to an internal development issue. label Oct 22, 2024
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