Error at step2 running gene-based testing: has N = 0 (mismatch with header block)

weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0

187 stars 72 forks source link

Error at step2 running gene-based testing: has N = 0 (mismatch with header block) #383

Closed xmduumich closed 2 years ago

xmduumich commented 2 years ago

Dear Wei Zhou,

When running SAIGE-GENE we observed this error message:

ERROR: has N = 0 (mismatch with header block)

I cannot find documentation to interpret or troubleshoot what cause this. Could you help me to figure out what it means and how to resolve it?

Here I attach the .log file from running step2_SPAtests.R.

step2_GB_PDFF_4_7_QCed_chr22.log Thank you for your help!

weizhouUMICH commented 2 years ago

Sorry for my late reply.

We have just released a new version 1.0.0. It has computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/

The program will be maintained by multiple SAIGE developers there. Please feel free to try the version 1.0.0 and report issues if any.

Thanks! Wei