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sirius-ms / sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
GNU Affero General Public License v3.0
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Error when importing .mzml files #209

Open sra34 opened 1 month ago

sra34 commented 1 month ago

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!

MartinHoffmannJena commented 1 month ago

Thank you for the detailed report, we are looking at this

sra34 commented 1 week ago

Hi there -- I downloaded the latest release (v 6.0.7) and imported the files again. I got the same error message but it seemed to work and progress to the next step. I am not sure if I trust it though. Any thoughts? Would you be able to test the files included in the above comment with the newest version release and see how it looks?

Thank you for your continued support.