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weizhouUMICH / SAIGE

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Error in step2 of saige gene for some genes in group file #396

Closed aokulabasile closed 2 years ago

aokulabasile commented 2 years ago

Hello,

I am encountering the following error when running step 2 of Saige GENE v 0.42.1:

"Error in array(a, dim = c(nrow(Gmat), ncol(Gmat))) : object 'a' not found Calls: SPAGMMATtest -> groupTest -> array Execution halted"

I've attached the log file and the group file to this issue. As you can see SAIGE-GENE runs successfully for a a number of genes in the group file until it gets to gene ADAM12 where it encounters the above error. I can't figure it out what it is about this gene that is causing the error. As recommended, variants are sorted by position, and follow the recommended variant naming of chrX:POS_REF/ALT. Any advice would be greatly appreciated.

Group file: chr10_r2_above_0.3.dose_samps.renamed_sample.subset_n393.vep_annotated_groupfile.txt

Log file: saige_gene_assoc_test_17547499_1.log

Thank you!

weizhouUMICH commented 2 years ago

Sorry fo the 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