Error while working with quality metrics

usegalaxy.org support
,
1

Hope you will be doing well.

I am facing some problems in QC metrics the said message is like

Fatal error: Exit code 1 ()
Error in QualityControl(args$dataMatrix_in, args$sampleMetadata_in, args$variableMetadata_in, :

Warning : no ‘pool’ detected in ‘sampleType’ variable (sample meta-data) !
CV can not be calculated.
there are pool samples in my smple metadata file with the name QC1 and QC2 but I dont know why it is still showing this.

after that i give it another try with following solution changing name QC1 and QC2 to pool1 and pool2 in sampleType colounm but it still showing error
Fatal error: Exit code 1 ()
Error in cor.test.default(dilVn, varVn) : not enough finite observations
Calls: QualityControl … qualityMetricsF -> apply -> FUN -> cor.test -> cor.test.default
Execution halted

2

Welcome, @Ahsan

For clarification, please confirm:

  1. Are you actually working at Galaxy Main https://usegalaxy.org? Check the URL. If a different public Galaxy server, please post back the URL. If your own Galaxy, share a bit about it (source? new?)
  2. What is the exact name and version of the tool? Find this at the very top of the tool form and post it back.

The second error could be related to the content, but more likely there is a formatting problem with the inputs that is contributing to both errors, even with the changes. If you are following a tutorial, please be sure to share that, too (plus which step and if using the tutorial data or your own).

Thanks!

3

Hey Jennifer,

Thanks for your response.

I have solve this problem somehow but at the same time I am facing other problem

well before going to other I will answer your queries.

  • Are you actually working at Galaxy Main https://usegalaxy.org? Check the URL. If a different public Galaxy server, please post back the URL. If your own Galaxy, share a bit about it (source? new?)
    **Here is the URL : toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/2.1.2. **

  • What is the exact name and version of the tool? Find this at the very top of the tool form and post it back.
    THE exact name of tool is in LCMS-preprocessing-quality control-batch correction version is 2.12

Now In batch correction, I am facing this problem with the following error message

Fatal error: Exit code 1 () Error in if (sd(qcp) == 0 | sd(spl) == 0) { : missing value where TRUE/FALSE needed Calls: norm_QCpool -> normlinear -> ok_norm Execution halted

Thanks,

Ahsan

1 Like
4

Hi @Ahsan

Ok, glad you resolved the original problem.

The Galaxy server you are working at is still not clear. You posted back a link to the tool in the ToolShed, not the server URL. This is the “https://” address in your browser window.

I could take a guess about which server but that won’t help directly. We may need to get you connected with the support team from whatever server you are working at since it isn’t clear if these are usage issues or actual tool bugs.

Although, just from reviewing your next error, it looks like another input problem: “missing value” is the clue. And you didn’t state the full tool name/version for the new tool that is failing.

If you want help, 1) specify the server URL and 2) copy and paste the full tool name/version as it comes up on the top of the tool form, exactly and without reformatting. Specifics matter when trying to troubleshoot.

Thanks!