GSL/cblas

[heinin]

Which GSL version are you using? I have problems with permutation using GSL 2.4.

Edit:

Apparently, the issue is not with GSL but perhaps with my data. The error only occurs with permutation:

Processing gene [OR4F5]

• Number of variants in cis = 458
• Best correlation = -0.9987
• Number of permutations = 69 / 1000
  gsl: simplex2.c:372: ERROR: non-finite function value encountered
  Default GSL error handler invoked.
  Aborted

I've tried to run this on Redhat and Ubuntu, using FastQTL-2.184.linux.tgz binary and by compiling myself, as well as the GTEx eQTL Docker image. It always fails at the same point. Any ideas on what could be wrong and how to proceed?

Thank you!

Best,

Heini

[ivlachos]

Hi @heinin,

Did you make any progress on this?

I believe this happens for genes with low variance but I'm still not 100% certain that filtering those is enough.

[hnaeem]

Dear @ivlachos

I'm running permutation pass with FastQTL/2.184. However, the tool is giving the following error message:
Processing gene [ENSG00000252645_RNU7-111P_snRNA]

• Number of variants in cis = 5901
• Best correlation = 1.0000
• Number of permutations = 100 / 197
  gsl: beta.c:44: ERROR: domain error
  Default GSL error handler invoked.
  Aborted

Any help will be appreciated.