1156 [INFO ] Renaming rpt dir on error to: ./GSEA/c5/WT1000UVvsSFA1000UV72h_Gsea

[Hongwei Tang]

Dear GSEA staff,

    I am running GSEA to analyze UV-induced gene differentiate expression analysis in pathways. I totally created 18 pairs of sample datasets (.gct, .cls). 14 of them are running smoothly and get the results, but four of them failed and give the following error information (I only give one sample):

1156 [INFO ] Renaming rpt dir on error to: ./GSEA/c5/WT1000UVvsSFA1000UV72h_Gsea/error_my_analysis.Gsea.1524615070908

The command I used as follows:

java -cp ./gsea3.0.jar xtools.gsea.Gsea -res  WT1000UVvsSFA1000UV_Gsea.gct -cls WT1000UVvsSFA1000UV_Gsea.cls -gmx c5.all.v6.1.symbols.gmt -collapse false -out ./GSEA/c5/WT1000UVvsSFA1000UV_Gsea  -gui false -nperm 1000 -permute gene

  

    I create the .gct and .cls files using the same R pipeline. I check the trouble files again and again and can't find any errors.

    I saw that Richard posted this bug before and can't find any solution to fix it.

  

   

Look forward to hearing from you.

Thank you first,

Best,

Hongwei

[Hongwei Tang]

Hi there, the issue has been diagnosed as follows. I posted it just in case some of our relatives walk around.

check .cls files:

scenario 1:  this one is correct and you are safe.
10 2 1
# T N
T T T T N T N N N N


otherwise
scenario 2:
10 2 1
# N T #see this line!!!!!!!!!!!!!!
T T T T N T N N N N
 You will get the above error message  and blocked.

Best,

Hongwei

[David Eby]

Hi Hongwei,

I'm glad you were able to find the issue; thanks for following up to the forum in case others bump into a similar issue.  

For anyone else seeing this error, I should mention that GSEA renames the analysis directory for just about any error and not only cases like the one mentioned here.  The key to finding the problem is usually found in the analysis log.  In the GSEA UI, that can be found by clicking the [+] symbol in the lower part of the window frame.  At the command-line it should be part of the console output.

Regards,

David

David Eby
Consultant
Cancer Informatics Development
Broad Institute of MIT and Harvard
415 Main St, Cambridge, MA 02142, USA
http://www.broadinstitute.org/cancer
http://www.gsea-msigdb.org
https://twitter.com/GSEA_MSigDB
https://twitter.com/GenePattern

[prashant...@gmail.com]

Hi David

This is regarding the same error: I am using .TXT files and get the same error. What should I do? I am analysing 2 control replicate datasets against 2 transgenic replicate datasets 

Thanks 

Prashanti

[David Eby]

Hi Prashanti,

As noted in the reply to Hongwei, GSEA will rename the directory for just about any error and so it's difficult to know what's wrong in your specific case without more information.  

If your case is similar to that one, note that the CLS file format is very particular: that problem was solved by re-ordering the class names on line 2.  See that Data Formats page in our Help Wiki for more information.

If your case is different from that one, we'll need more information about what's going wrong to help, perhaps including your input files.  I would suggest first closely reviewing your file content with respect to that Help page.

Regards,

David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

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[leo2...@gmail.com]

Dear GSEA staff,

I am now running the loaded data including both cls. and gct. file and the parameters I set were all correct but ended up showing "Renaming rpt dir on error to...".

I have checked "GSEA User Guide" and "Document wiki", but still couldn't figure out the solution to the problem. Did I miss anything or any command should be added but not?

Thanks,

Best regard,

Leo

Hongwei Tang於 2018年4月26日星期四 UTC+8上午12時36分33秒寫道：

[David Eby]

Hi Leo,

Have you read my responses to Hongwei and Prashanti up-thread?  If so, it should be clear that this message is just an indication an error occurred but is not the error itself.

Look at the whole log of the analysis run to see the actual error.  That's available by clicking the [+] icon in the lower part of the GSEA window frame.  We can try to use that info to troubleshoot the issue, but nothing further can be done with what you've provided.

Regards,

David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

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[劉立威]

Hi David!

Thanks for your response and advice. I've clicked the + icon at the bottom of the running page next to the clock.

I scrolled down to the bottom part of the frame and the application message showed "2201202  [ERROR ] - Tool exec error

xtools.api.param.BadParamException: The collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub/gsea/annotations_versioned/Mouse_Agilent_SurePrint_g3_ge_8x60k_to_Human_Orthologs_MSigDB.v7.1.chip"

Then, I changed the chip platform to the human version and it succeeded. My Q is the gene dataset I ran was from a mouse gene array. Therefore I selected the mouse one rather than the human one.

Thanks, 

Best regards,

Leo

David Eby <e...@broadinstitute.org> 於 2020年5月21日 週四 上午6:30寫道：

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[Anthony Castanza]

Hi Leo,

If you're sure the data was from a mouse array, and hadn't undergone any sort of orthology conversion before it made it in to your hands, then frankly, this shouldn't have worked and I'd suspect that it didn't actually work correctly.

Would you mind sending us a screenshot of your input parameters and a sample of your input file (no need to send the whole thing, the first dozen or so lines pasted into a new document would be sufficient) so that we can investigate the identifiers further?

You also might want to start a new thread here so we don't keep notifying the other people upthread with this unrelated issue.

Thanks,

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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[劉立威]

Hi Anthony,

I have checked the platform type I ran and it should be the human one as you mentioned the orthology conversion.

Thanks,

Leo

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