Error when importing .mzml files #209
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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!
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