How to set the labelling method (TMT10/11, iTRAQ, ...) on command line

[steve-lefever]

Hi,

Can the labelling method be set when running Reporter command line? If so, how is this done? I can't find that info when using either PathSettingsCLI or ReporterCLI

Kind regards,
Steve

[steve-lefever]

Hi,

You can close the issue, I found that you can use -method for this while using eu.isas.reporter.cli.ReporterCLI. Don't know why I missed it.

Kind regards,
Steve

[hbarsnes]

Hi Steve,

You can find all of the ReportCLI command line options here: https://github.com/compomics/reporter/blob/master/src/main/java/eu/isas/reporter/cli/ReporterCLIParameters.java

I assume that methods is the one you are interested in.

Best regards,
Harald

[hbarsnes]

You can close the issue, I found that you can use -method for this while using eu.isas.reporter.cli.ReporterCLI. Don't know why I missed it.

I think we posted at the same time. :)

[steve-lefever]

Hi Harald,

I'm now getting this error message:

root@b7d984e774e8:/var/tmp/test/samples/19CPTAC_HNSCC_Proteome_JHU_20191003# java -Xmx250G -Xms250G -XX:MaxMetaspaceSize=250G -cp /var/tmp/Reporter-0.10.4/Reporter-0.10.4.jar eu.isas.reporter.cl
i.ReporterCLI -method TMT11 -id /var/tmp/test/samples/19CPTAC_HNSCC_Proteome_JHU_20191003/19CPTAC_HNSCC_Proteome_JHU_20191003.psdb -out /var/tmp/test/samples/19CPTAC_HNSCC_Proteome_JHU_20191003/19CPTAC_HNSCC_Proteome_JHU_20191003_reporter.psdb -temp_folder /var/tmp/test/temp/
Path configuration completed.
Fri Oct 06 12:54:25 GMT 2023 Opening PeptideShaker Project. Please Wait...
Fri Oct 06 12:54:26 GMT 2023 An error occurred while reading:
/var/tmp/test/samples/19CPTAC_HNSCC_Proteome_JHU_20191003/19CPTAC_HNSCC_Proteome_JHU_20191003.psdb.

Please verify that the Reporter version used to create
the file is compatible with your version of Reporter.

The .psdb file was created using PeptideShaker v2.2.25, and no error message popped up when running PeptideShaker.

Kind regards,
Steve

[hbarsnes]

Hi Steve,

The PeptideShaker-Reporter compatibility is a bit complicated. Basically, you have to make sure that you are using versions that have the same backend code. However, PeptideShaker v2.2.25 should be compatible with Reporter 0.10.4 (according to the release notes).

Are there any errors in the Reporter log file?

Best regards,
Harald

[steve-lefever]

Hi Harald,

Where's the log located?

Kind regards,
Steve

[hbarsnes]

Hi Steve,

Where's the log located?

It should be in the Reporter-X.Y.Z\resources folder.

Best regard,
Harald

[steve-lefever]

Hi Harald,

The log file is stating this:

Fri Oct 06 13:59:47 GMT 2023: Reporter version 0.10.4.
Memory given to the Java virtual machine: 268435456000 b.
Total amount of memory in the Java virtual machine: 268435456000 b.
Free memory: 268368347136 b.
Java version: 11.0.20.1.
org.apache.commons.cli.MissingArgumentException: Missing argument for option: method
        at org.apache.commons.cli.DefaultParser.checkRequiredArgs(DefaultParser.java:231)
        at org.apache.commons.cli.DefaultParser.handleOption(DefaultParser.java:394)
        at org.apache.commons.cli.DefaultParser.handleShortAndLongOption(DefaultParser.java:474)
        at org.apache.commons.cli.DefaultParser.handleToken(DefaultParser.java:542)
        at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:712)
        at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:679)
        at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:660)
        at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:1144)

I've checked and the variable supplied to the -method argument was indeed empty.

Kind regards,
Steve

[steve-lefever]

Hi Harald,

I'm now receiving this error message:

Fri Oct 06 14:06:49 GMT 2023 The reporter quantification methods to use could not be inferred, please specify a method from the isotopic correction file as command line parameter.

Reporter is apparently not using the default values for this. Do you have a template for the .xml file that needs to be supplied as part of the -isotopes argument?

Kind regards,
Steve

[steve-lefever]

Hi Harald,

Could it be that Reporter isn't recognizing the value I've supplied for the -method argument, which results in the error message above? I'm currently using -method TMT11. What are the allowed values for the -method argument?

Kind regards,
Steve

[hbarsnes]

Hi Steve,

The default methods xml file is found in "Reporter-X.Y.Z\resources\conf\defaultMethods.xml" where you will also find the names of the supported methods. The one you are looking for seems to be "TMT 11-plex".

Best regards,
Harald