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genetics-statistics / GEMMA

Genome-wide Efficient Mixed Model Association
https://github.com/genetics-statistics/GEMMA
GNU General Public License v3.0
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Errors when running GEMMA in an SoS step but ok in command line #258

Open zhangbs92 opened 3 years ago

zhangbs92 commented 3 years ago

Describe the bug ERROR: Enforce failed for file_kin /home/bz2437/UKB_genotype_data/fam_folder/output/ascertain_fam_1.cXX.txt: open file in src/param.cpp at line 905 in CheckParam

To Reproduce

Expected behavior

Screenshots

I tried to call gemma in one step of my SoS code. In dryrun mode, my sos code works fine:

image

Even I copied and paste the command lines and ran it in terminal, it worked perfectly:

image image

However, when I run the whole SoS workflow, I saw errors like this:

image

Does anyone know what the problem is?

Thanks, Bingsong

Additional context Add any other context about the problem here.

Check list:

  1. [X] I have found an issue with GEMMA
  2. [ ] I have searched for it on the issue tracker (incl. closed issues)
  3. [ ] I have searched for it on the mailing list
  4. [ ] I have tried the latest release of GEMMA
  5. [ ] I have read and agreed to below code of conduct
  6. [ ] If it is a support/install question I have posted it to the mailing list
  7. [ ] If it is software development related I have posted a new issue on the issue tracker or added to an existing one
  8. [ ] In the message I have included the output of my GEMMA run
  9. [ ] In the message I have included the relevant .log.txt file in the output directory
  10. [ ] I have made available the data to reproduce the problem (optional)

To find bugs the GEMMA software developers may ask to install a development version of the software. They may also ask you for your data and will treat it confidentially. Please always remember that GEMMA is written and maintained by volunteers with good intentions. Our time is valuable too. By helping us as much as possible we can provide this tool for everyone to use.

pjotrp commented 3 years ago

Are your nodes trying to open the same file? Make sure they are uniquely named, such as gemma-wrapper does.