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)
I am using Sirius version 5.5.7, and I have encountered an issue while trying to import two MGF files, f1.mgf and f11.mgf, which have identical content. Surprisingly, the import process works fine for f1.mgf, but I receive an error when attempting to import f11.mgf. The error message I receive is as follows:
For input string: "MS2" at java.base/java.lang.NumberFormatException.forInputString(Unknown Source) at java.base/java.lang.Integer.parseInt(Unknown Source) at java.base/java.lang.Integer.parseInt(Unknown Source) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.handleKeyword(MgfParser.java:202) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.readNext(MgfParser.java:245) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.addNextEntry(MgfParser.java:114) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.hasNext(MgfParser.java:98) at de.unijena.bioinf.babelms.mgf.MgfParser.parse(MgfParser.java:329) at de.unijena.bioinf.babelms.mgf.MgfParser.parse(MgfParser.java:42) at de.unijena.bioinf.babelms.GenericParser.parse(GenericParser.java:177) at de.unijena.bioinf.babelms.GenericParser$1.<init>(GenericParser.java:84) at de.unijena.bioinf.babelms.GenericParser.parseIterator(GenericParser.java:76) at de.unijena.bioinf.babelms.GenericParser.parseIterator(GenericParser.java:72) at de.unijena.bioinf.projectspace.MS2ExpInputIterator.fetchNext(MS2ExpInputIterator.java:101) at de.unijena.bioinf.projectspace.MS2ExpInputIterator.<init>(MS2ExpInputIterator.java:71) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.importMsParserInput(InstanceImporter.java:149) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.importMultipleSources(InstanceImporter.java:118) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.compute(InstanceImporter.java:107) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.compute(InstanceImporter.java:94) at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source)
I am wondering what could be the reason behind this issue and how can I resolve it? It seems that there is a problem parsing the MGF file, specifically with the "MS2" string. Both files have similar content, so I expected them to behave the same way during the import process. Any insights or suggestions on how to overcome this issue would be greatly appreciated.
Dear Sirius team,
I am using Sirius version 5.5.7, and I have encountered an issue while trying to import two MGF files, f1.mgf and f11.mgf, which have identical content. Surprisingly, the import process works fine for f1.mgf, but I receive an error when attempting to import f11.mgf. The error message I receive is as follows:
For input string: "MS2" at java.base/java.lang.NumberFormatException.forInputString(Unknown Source) at java.base/java.lang.Integer.parseInt(Unknown Source) at java.base/java.lang.Integer.parseInt(Unknown Source) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.handleKeyword(MgfParser.java:202) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.readNext(MgfParser.java:245) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.addNextEntry(MgfParser.java:114) at de.unijena.bioinf.babelms.mgf.MgfParser$MgfParserInstance.hasNext(MgfParser.java:98) at de.unijena.bioinf.babelms.mgf.MgfParser.parse(MgfParser.java:329) at de.unijena.bioinf.babelms.mgf.MgfParser.parse(MgfParser.java:42) at de.unijena.bioinf.babelms.GenericParser.parse(GenericParser.java:177) at de.unijena.bioinf.babelms.GenericParser$1.<init>(GenericParser.java:84) at de.unijena.bioinf.babelms.GenericParser.parseIterator(GenericParser.java:76) at de.unijena.bioinf.babelms.GenericParser.parseIterator(GenericParser.java:72) at de.unijena.bioinf.projectspace.MS2ExpInputIterator.fetchNext(MS2ExpInputIterator.java:101) at de.unijena.bioinf.projectspace.MS2ExpInputIterator.<init>(MS2ExpInputIterator.java:71) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.importMsParserInput(InstanceImporter.java:149) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.importMultipleSources(InstanceImporter.java:118) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.compute(InstanceImporter.java:107) at de.unijena.bioinf.projectspace.InstanceImporter$ImportInstancesJJob.compute(InstanceImporter.java:94) at de.unijena.bioinf.jjobs.BasicJJob.call(BasicJJob.java:117) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source)I am wondering what could be the reason behind this issue and how can I resolve it? It seems that there is a problem parsing the MGF file, specifically with the "MS2" string. Both files have similar content, so I expected them to behave the same way during the import process. Any insights or suggestions on how to overcome this issue would be greatly appreciated.
Thank you in advance for your help!
f1.zip f11.zip
yh sheng