Unmatched arguments from index 6: 'structure', '--database', 'pubchem'

[spzheng0908]

Hi, I just installed a new version of SIRIUS (6.1.0), however when I try to run the structure command (similar to how is shown in the documentation) I got an error that structure is an unmatched argument (please see below). Can anyone help me? Thanks in advance for your help!

sirius -i ./33OPEs_spectrum_combined_lack13812.mgf -o ./Test_2.sirius formula fingerprint structure --database pubchem write-summaries --top-k-summary=10 --format=csv --output ./Test3

SEVERE: Unexpected Error!
picocli.CommandLine$UnmatchedArgumentException: Unmatched arguments from index 6: 'structure', '--database', 'pubchem'

[ts-dangelo]

I too have been getting those same bugs:

CSI:FingerID: Identifying Molecular Structures

sirius -i -o formula fingerprint structure --database pubchem

Apr 14, 2025 3:40:39 PM de.unijena.bioinf.ms.frontend.Run parseArgs
INFO: Running with following arguments: [--input, /input/222_sirius.mgf, --output, /output/222.csi.sirius, formula, fingerprint, --database, pubchem, write-summaries, --output, /output/222_csi]
Apr 14, 2025 3:40:39 PM de.unijena.bioinf.jjobs.JJob lambda$logDebug$13
FINE: <0>[InputExpanderJJob-0] Running post processing
Apr 14, 2025 3:40:39 PM de.unijena.bioinf.jjobs.JJob lambda$logDebug$13
FINE: <0>[InputExpanderJJob-0] Running cleanup
Apr 14, 2025 3:40:39 PM de.unijena.bioinf.jjobs.JJob lambda$logInfo$9
INFO: <1>[InputExpanderJJob-1] Expanding Input Files: '/input/222_sirius.mgf'...
Apr 14, 2025 3:40:39 PM de.unijena.bioinf.jjobs.JJob lambda$logInfo$9
INFO: <1>[InputExpanderJJob-1] ...Input Files successfully expanded!
Apr 14, 2025 3:40:39 PM de.unijena.bioinf.jjobs.JJob lambda$logDebug$13
FINE: <1>[InputExpanderJJob-1] Running post processing
Apr 14, 2025 3:40:39 PM de.unijena.bioinf.jjobs.JJob lambda$logDebug$13
FINE: <1>[InputExpanderJJob-1] Running cleanup
Apr 14, 2025 3:40:39 PM de.unijena.bioinf.ms.frontend.SiriusCLIApplication run
SEVERE: Unexpected Error!
picocli.CommandLine$UnmatchedArgumentException: Unknown options: '--database', 'pubchem'
at picocli.CommandLine$Interpreter.validateConstraints(CommandLine.java:13662)
at picocli.CommandLine$Interpreter.parse(CommandLine.java:13614)
at picocli.CommandLine$Interpreter.processSubcommand(CommandLine.java:13904)
at picocli.CommandLine$Interpreter.processArguments(CommandLine.java:13800)
at picocli.CommandLine$Interpreter.parse(CommandLine.java:13591)
at picocli.CommandLine$Interpreter.processSubcommand(CommandLine.java:13904)
at picocli.CommandLine$Interpreter.processArguments(CommandLine.java:13800)
at picocli.CommandLine$Interpreter.parse(CommandLine.java:13591)
at picocli.CommandLine$Interpreter.parse(CommandLine.java:13559)
at picocli.CommandLine$Interpreter.parse(CommandLine.java:13454)
at picocli.CommandLine.parseArgs(CommandLine.java:1552)
at de.unijena.bioinf.ms.frontend.Run.parseArgs(Run.java:82)
at de.unijena.bioinf.ms.frontend.SiriusCLIApplication.run(SiriusCLIApplication.java:143)
at de.unijena.bioinf.ms.frontend.SiriusCLIApplication.runMain(SiriusCLIApplication.java:77)
at de.unijena.bioinf.ms.middleware.SiriusMiddlewareApplication.main(SiriusMiddlewareApplication.java:222)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.springframework.boot.loader.launch.Launcher.launch(Launcher.java:102)
at org.springframework.boot.loader.launch.Launcher.launch(Launcher.java:64)
at org.springframework.boot.loader.launch.JarLauncher.main(JarLauncher.java:40)

I then tried without those options:

INFO: Running with following arguments: [--input, /input/222_sirius.mgf, --output, /output/222.csi.sirius, formula, fingerprint, structure, write-summaries, --output, /output/222_csi]
Apr 14, 2025 3:37:34 PM de.unijena.bioinf.jjobs.JJob lambda$logDebug$13
FINE: <0>[InputExpanderJJob-0] Running post processing
Apr 14, 2025 3:37:34 PM de.unijena.bioinf.jjobs.JJob lambda$logDebug$13
FINE: <0>[InputExpanderJJob-0] Running cleanup
Apr 14, 2025 3:37:34 PM de.unijena.bioinf.jjobs.JJob lambda$logInfo$9
INFO: <1>[InputExpanderJJob-1] Expanding Input Files: '/input/222_sirius.mgf'...
Apr 14, 2025 3:37:34 PM de.unijena.bioinf.jjobs.JJob lambda$logInfo$9
INFO: <1>[InputExpanderJJob-1] ...Input Files successfully expanded!
Apr 14, 2025 3:37:34 PM de.unijena.bioinf.jjobs.JJob lambda$logDebug$13
FINE: <1>[InputExpanderJJob-1] Running post processing
Apr 14, 2025 3:37:34 PM de.unijena.bioinf.jjobs.JJob lambda$logDebug$13
FINE: <1>[InputExpanderJJob-1] Running cleanup
Apr 14, 2025 3:37:34 PM de.unijena.bioinf.ms.frontend.SiriusCLIApplication run
SEVERE: Unexpected Error!
picocli.CommandLine$UnmatchedArgumentException: Unmatched argument at index 6: 'structure'
at picocli.CommandLine$Interpreter.validateConstraints(CommandLine.java:13662)
at picocli.CommandLine$Interpreter.parse(CommandLine.java:13614)
at picocli.CommandLine$Interpreter.processSubcommand(CommandLine.java:13904)
at picocli.CommandLine$Interpreter.processArguments(CommandLine.java:13800)
at picocli.CommandLine$Interpreter.parse(CommandLine.java:13591)
at picocli.CommandLine$Interpreter.processSubcommand(CommandLine.java:13904)
at picocli.CommandLine$Interpreter.processArguments(CommandLine.java:13800)
at picocli.CommandLine$Interpreter.parse(CommandLine.java:13591)
at picocli.CommandLine$Interpreter.parse(CommandLine.java:13559)
at picocli.CommandLine$Interpreter.parse(CommandLine.java:13454)
at picocli.CommandLine.parseArgs(CommandLine.java:1552)
at de.unijena.bioinf.ms.frontend.Run.parseArgs(Run.java:82)
at de.unijena.bioinf.ms.frontend.SiriusCLIApplication.run(SiriusCLIApplication.java:143)
at de.unijena.bioinf.ms.frontend.SiriusCLIApplication.runMain(SiriusCLIApplication.java:77)
at de.unijena.bioinf.ms.middleware.SiriusMiddlewareApplication.main(SiriusMiddlewareApplication.java:222)
at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
at java.base/java.lang.reflect.Method.invoke(Method.java:580)
at org.springframework.boot.loader.launch.Launcher.launch(Launcher.java:102)
at org.springframework.boot.loader.launch.Launcher.launch(Launcher.java:64)
at org.springframework.boot.loader.launch.JarLauncher.main(JarLauncher.java:40)

[MartinHoffmannJena]

Hi,

Please try:

formula fingerprint classes structure --database pubchem

[sdhsamira]

Hi

I had the same problem and it worked!