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stephenslab / susie-paper

Experiments on SuSiE ("sum of single effects") regression.
https://stephenslab.github.io/susie-paper
MIT License
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Error from fit_caviar and fit_finemap after updating to latest dsc 0.3.13 #5

Closed ZacZZZ closed 4 years ago

ZacZZZ commented 4 years ago

Hi Stephens lab,

I updated SoS, DSC and dscutils to the latest version.

And now I have error from running dsc susie.dsc --target run_comparison -o toy_comparison -c 8

Error in dscrutils::run_cmd(cmd) : 
  CAVIAR command failed (returned a non-zero exit status)
Calls: finemap_mcaviar ... lapply -> FUN -> single_core -> run_caviar -> <Anonymous>
Error in dscrutils::run_cmd(cmd) : 
  finemap command failed (returned a non-zero exit status)
Calls: finemap_mvar ... lapply -> FUN -> single_core -> run_finemap -> <Anonymous>

Are these version issues? Any suggestions will be helpful.

Thank you, Zac

ZacZZZ commented 4 years ago

The errors are gone with the -s all skipping command you suggested, but it is just not reporting the running time.

ZacZZZ commented 4 years ago

But they are different errors then stephenslab/dsc#211. Do you think it might affect the pipeline on other datasets?

gaow commented 4 years ago

@ZacZZZ most of issues you run into so far are DSC / dscrutils version issues but the particular issue about does not read like a version issue. It seems to suggest FINEMAP and CAVIAR command failed. Were you able to run FINEMAP and CAVIAR commands in the terminal without an error?

Yes -s all will use my existing results instead. But it does not mean you can run those commands fine. A good first place to start checking is to make sure those two executable programs work on your computer.

No promises and a fixed timeline for it, but we are in the process of updating the fine-mapping benchmark using latest version of DSC. That should remove most of the issues you have, when we get it done.

ZacZZZ commented 4 years ago

Both finemap and CAVIAR work on my command line with the example data provided by these two software. But I use the version in your Dockerfile. I will try update them later and let you know how it goes.

gaow commented 4 years ago

Defer it to #6

gaow commented 4 years ago

@ZacZZZ it turns out a regression bug that we now fixed in 0.4.0, if you pip install dsc -U on your desktop / cluster it should work even without using docker ...