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How to set the labelling method (TMT10/11, iTRAQ, ...) on command line #23
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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, |
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 Best regards, |
I think we posted at the same time. :) |
Hi Harald, I'm now getting this error message:
The .psdb file was created using PeptideShaker v2.2.25, and no error message popped up when running PeptideShaker. Kind regards, |
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, |
Hi Harald, Where's the log located? Kind regards, |
Hi Steve,
It should be in the Reporter-X.Y.Z\resources folder. Best regard, |
Hi Harald, The log file is stating this:
I've checked and the variable supplied to the -method argument was indeed empty. Kind regards, |
Hi Harald, I'm now receiving this error message:
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, |
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 Kind regards, |
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, |
Hi Harald, I'm still having problems generating both the PeptideShaker and Reporter reports. I also noticed that the psdb files generated by PeptideShaker and Reporter have exactly the same size, is that possible? While generating the report PeptideShaker gives me this error message:
And Reporter gives me this message :
With this in
Is it possible that something is wrong with the initial psdb file generated by PeptideShaker, although it doesn't crash or generate an error when it runs and creates the file? I'm running SearchGUI-4.3.1, PeptideShaker 2.2.25 and Reporter 0.10.4 Kind regards, |
Hi Steve, I would recommend updating to SearchGUI v4.3.1, PeptideShaker v3.0.1 and Reporter v0.12.0 to see if that helps. I think I would also recommend updating to a more recent version of OpenJDK. As for the Reporter exception, can you show me the command line you are using? And does the given FASTA file exist? Best regards, |
Hi Harald, Can you tell me what files must be present in the input folder when running the specific tools? For example when running Reporter to generate the report it seems that the fasta file must be available, however this is nowhere specified for any of the tools in the available documentation, nor can it be determined from the command line arguments associated with each of the tools. Kind regards, |
Hi Steve,
If you use a PeptideShaker psdb file as input to Reporter the spectrum and FASTA files have to either be available at the locations used when generating the PeptideShaker project or located in the same folder as the psdb file. You can get around this by exporting the PeptideShaker project as a zip file and using this as input to Reporter. A similar trick can be used for PeptideShaker where the https://github.com/compomics/searchgui/wiki/SearchCLI#optional-output-compression-parameters options can be used to include the spectrum and FASTA files in the SearchGUI output. Best regards, |
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
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