Unmatched argument

[Coayala]

Good evening,

I just installed a new version of SIRIUS (5.5.7), however when I try to run the formula and structure command (similar to how is shown in the documentation) I got an error that structure is an unmatched argument (please see below)

> sirius -i <input> -o <projectspace> formula structure --database pubchem

============>
Sep 29, 2022 6:21:30 AM org.apache.commons.beanutils.FluentPropertyBeanIntrospector introspect
INFO: Error when creating PropertyDescriptor for public final void org.apache.commons.configuration2.AbstractConfiguration.setProperty(java.lang.String,java.lang.Object)! Ignoring this property.
INFO    06:21:30 - Sirius Workspace Successfull initialized at: /home/u29/cayalaortiz/.sirius-5.5
INFO    06:21:30 - You run SIRIUS 5.5.7
INFO    06:21:30 - Sirius was compiled with the following ILP solvers: GLPK-v1.7.0 (included), Gurobi-v9.1.1, CPLEX-v12.7.1, COIN-OR-v1.17.3
INFO    06:21:30 - Treebuilder priorities loaded from 'sirius.properties' are: [GUROBI, CPLEX, CLP, GLPK]
INFO    06:21:30 - CPU check done. 22 cores that handle 45 threads were found.
INFO    06:21:32 - Web API initialized.
INFO    06:21:32 - Running with following arguments: [-i, test_data/grouped_mgf/group_1.mgf, -o, test_data/SIRIUS_output/group_1, formula, structure, write-summaries]
INFO    06:21:32 - Job manager successful initialized with 22 CPU thread(s) and 3 IO thread(s).
FINE    06:21:32 - <0>[InputExpanderJJob-0] Running post processing
FINE    06:21:32 - <0>[InputExpanderJJob-0] Running cleanup
INFO    06:21:32 - <1>[InputExpanderJJob-1] Expanding Input Files: 'test_data/grouped_mgf/group_1.mgf'...
INFO    06:21:32 - <1>[InputExpanderJJob-1] ...Input Files successfully expanded!
FINE    06:21:32 - <1>[InputExpanderJJob-1] Running post processing
FINE    06:21:32 - <1>[InputExpanderJJob-1] Running cleanup
Unmatched argument at index 5: 'structure'
Did you mean: passatutto or rerank-formulas?
INFO    06:21:32 - CLI shut down hook: SIRIUS is cleaning up threads and shuts down...
INFO    06:21:32 - Try to delete leftover jobs on web server...

The same happens whether or not I add the write-summaries command. Thanks in advance for your help

[mfleisch]

Good catch. The docu is just noch up-to-date here. SInce SIRIUS 5 fingerprint prediction is a separate step and no longer included in the structure database search command. For SIRIUS 5 the command would be:

sirius -i <input> -o <projectspace> formula fingerprint structure --database pubchem

[Coayala]

Thanks a lot for your help. It is working now.