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compomics / reporter

Protein quantification based on reporter ions
http://compomics.github.io/projects/reporter.html
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Unrecognized option: -id, -isotopes, -methods_file #11

Closed Steynd08 closed 3 years ago

Steynd08 commented 5 years ago

Good day,

I am running Reporter-0.7.15 on a server and I have installed it on each computer node, so all should be running fine. According the the info page in cmd line for Reporter the input options "-id" is mandatory, and either "-isotopes" OR "-methods_file" should identify the .xml file with isotope specifications ( I have tried both, with reference to #6 recommendations). Except that the following errors are still occurring. What could the reason for this be? Are there any alternate options?

Fri May 03 10:36:31 SAST 2019: Reporter version 0.7.15. Memory given to the Java virtual machine: 28631367680 b. Total amount of memory in the Java virtual machine: 2022178816 b. Free memory: 1958823720 b. Java version: 1.8.0_181. org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -id at org.apache.commons.cli.Parser.processOption(Parser.java:363) at org.apache.commons.cli.Parser.parse(Parser.java:199) at org.apache.commons.cli.Parser.parse(Parser.java:85) at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:815)

Fri May 03 10:38:12 SAST 2019: Reporter version 0.7.15. Memory given to the Java virtual machine: 28631367680 b. Total amount of memory in the Java virtual machine: 2022178816 b. Free memory: 1958823720 b. Java version: 1.8.0_181. org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -isotopes at org.apache.commons.cli.Parser.processOption(Parser.java:363) at org.apache.commons.cli.Parser.parse(Parser.java:199) at org.apache.commons.cli.Parser.parse(Parser.java:85) at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:815)

Fri May 03 10:41:11 SAST 2019: Reporter version 0.7.15. Memory given to the Java virtual machine: 28631367680 b. Total amount of memory in the Java virtual machine: 2022178816 b. Free memory: 1958823720 b. Java version: 1.8.0_181. org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -methods_file at org.apache.commons.cli.Parser.processOption(Parser.java:363) at org.apache.commons.cli.Parser.parse(Parser.java:199) at org.apache.commons.cli.Parser.parse(Parser.java:85) at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:815)

Here is my bash command(s): java -cp $REPORTER eu.isas.reporter.cli.ReporterCLI -in "/nlustre/users/dwilson/peptideshaker_output/MGF_100/FU_100/CDK/HDB/Rep1/ps_output_CDK100HDB_SM_FT_1_1.cpsx" -methods_file "/nlustre/users/dwilson/ZippedData/defaultMethods.xml" -out "/nlustre/users/dwilson/Reporter_Output/MGF_100/FU_100/CDK/HDB/FT/Rep1/Quant_output_CDK100HDB_SM_FT_1_1.cpsx" -zip "/nlustre/users/dwilson/Reporter_Output/MGF_100/FU_100/CDK/HDB/FT/Rep1/Quant_output_CDK100HDB_SM_FT_1_1.zip" -threads 8 -temp_folder "/nlustre/users/dwilson/Reporter_Output/TEMPSTORE/HDB/FU_100/FT/Rep1" -log "/nlustre/users/dwilson/Reporter_Output/logs/HDB/FU_100/FT/Rep1"

There is only 1 method listed in the methods file. Thanks! Denise

hbarsnes commented 5 years ago

Hi Denise,

I think you are mixing ReporterCLI and ReportCLI. :)

These have different roles and different parameters. Run eu.isas.reporter.cli.ReporterCLI and eu.isas.reporter.cli.ReportCLI to see all the options for the two command lines.

Best regards, Harald

Steynd08 commented 5 years ago

Hi Harald,

Thanks for your response. I understand why you would think I am confusing the two- because my code above has "-in" instead of "-id". I tried both out of desperation. Is there another reason why you say I am confusing the two?

The options for the command line for ReporterCLI are: _java -cp $REPORTER eu.isas.reporter.cli.ReporterCLI | grep "-"

-id The PeptideShaker project (.cpsx or .zip). -isotopes The isotope correction factors file (.xml file). Default values used if not provided. It is strongly advised to provide the values corresponding to the labelling kit used during the experiment. -methods_file Path to the isotope correction factors file containing the quantification methods including isotopic correction factors. Default values used if not provided. -method The reporter ion quantification method to use from the isotopic methods file in case multiple methods are listed in the file. Inferred from the identification parameters if not provided. -out Output file to save the project. -zip Exports the entire project as a zip file in the file specified. -threads Number of threads to use for the processing, default: the number of cores on the machine. -temp_folder A folder for temporary file storage. Use only if you encounter problems with the default configuration. -idparams The identification parameters file to use.

So, I enter the command: _java -cp $REPORTER eu.isas.reporter.cli.ReporterCLI -id "/nlustre/users/dwilson/peptideshaker_output/MGF_100/FU_100/CDK/HDB/Rep1/ps_output_CDK100HDB_SM_FT_1_1.cpsx" -isotopes "/nlustre/users/dwilson/ZippedData/defaultMethods.xml" -out "/nlustre/users/dwilson/Reporter_Output/MGF_100/FU_100/CDK/HDB/FT/Rep1/Quant_output_CDK100HDB_SM_FT_1_1.cpsx" -zip "/nlustre/users/dwilson/Reporter_Output/MGF_100/FU_100/CDK/HDB/FT/Rep1/Quant_output_CDK100HDB_SM_FT_1_1.zip" -threads 7 -temp_folder "/nlustre/users/dwilson/Reporter_Output/TEMPSTORE/HDB/FU_100/FT/Rep1" -log "/nlustre/users/dwilson/Reporter_Output/logs/HDB/FU_100/FT/Rep1" -id_params "/nlustre/users/dwilson/ZippedData/FU_hybrid_stablemodsFULL.par"

But my error output is still: _Fri May 03 16:01:37 SAST 2019: Reporter version 0.7.15. Memory given to the Java virtual machine: 28631367680 b. Total amount of memory in the Java virtual machine: 2022178816 b. Free memory: 1969382904 b. Java version: 1.8.0181. org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -id at org.apache.commons.cli.Parser.processOption(Parser.java:363) at org.apache.commons.cli.Parser.parse(Parser.java:199) at org.apache.commons.cli.Parser.parse(Parser.java:85) at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:815)

Hope you can help.

Regards, Denise

hbarsnes commented 5 years ago

Hi Denise,

I understand why you would think I am confusing the two- because my code above has "-in" instead of "-id". I tried both out of desperation. Is there another reason why you say I am confusing the two?

That was indeed the main reason. But it turns out that it was me and not you confusing the two, as you can see from the release notes for the latest version from February: https://github.com/compomics/reporter/wiki/ReleaseNotes.

So if you update to Reporter v0.7.17 the options should again work as wanted.

Best regards, Harald

Steynd08 commented 5 years ago

Hi Harald,

Thank you for the advice.

My Prof has attempted to make the update on the servers, but we are struggling to get it to work from the source code.

Do you perhaps have an available copy of Reporter v.0.7.17 that has already been built OR specific build-instructions for our reference?

Thank you for your assistance.

Kindest Regards,

On Fri, May 3, 2019 at 6:16 PM Harald Barsnes notifications@github.com wrote:

Hi Denise,

I understand why you would think I am confusing the two- because my code above has "-in" instead of "-id". I tried both out of desperation. Is there another reason why you say I am confusing the two?

That was indeed the main reason. But it turns out that it was me and not you confusing the two, as you can see from the release notes for the latest version from February: https://github.com/compomics/reporter/wiki/ReleaseNotes.

So if you update to Reporter v0.7.17 the options should again work as wanted.

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/reporter/issues/11#issuecomment-489153682, or mute the thread https://github.com/notifications/unsubscribe-auth/AJDXLZ7E5KU5LDD4OCCZDETPTRQMVANCNFSM4HKSGWNA .

-- 072 832 7718 steynd08@gmail.com

hbarsnes commented 5 years ago

Hi Denise,

There should be no need to build Reporter from the source unless you want to make change to the code.

Reporter v0.7.17 (or now actually v0.7.18) can be downloaded from http://compomics.github.io/projects/reporter.html or directly from GitHub at https://github.com/compomics/reporter. Just click the download link.

Best regards, Harald

Steynd08 commented 5 years ago

Hi Harald,

The server route is not working (no error log), so I tried the software on my desktop instead. ReporterGUI v0.7.19 is saying it is not compatible with my Peptideshaker projects (v1.16.36) ran in April this year. I have also tried Reporter version 0.7.7 (May 2017) and 0.7.17 (April 2019), with the same error, i.e. unable to open project due to PeptideShaker version compatibility issue.

I would not like to rerun the PeptideShaker jobs (for which I have exported reports), do you perhaps have other versions of Reporter on archive, that I can try to overcome the compatibility issue?

Regards, Denise

hbarsnes commented 5 years ago

Hi Denise,

You can find all the old versions of Reporter here: http://genesis.ugent.be/maven2/eu/isas/reporter/Reporter/.

Best regards, Harald