Hello,
I am trying to run an analysis using Saige on a complete dataset (480k) on chromosome X. While creating a null model, I encountered a "memory not mapped" error. I have reported this error to the helpdesk and would also like to ask if anyone has encountered this issue before. I understand that running an analysis on a complete dataset can be cumbersome, but I am only using one chromosome (X) with approximately 30k variants for the null model, so I assume it shouldn't be an issue. I am looking for suggestions; please let me know if you have any advice.
I was able to get the results for a smaller subset of the 50k dataset but running the same in the complete dataset is problematic.
Regards
Akhil
Thank you so much for the help. I think it's a version issue. Most recent versions can run analysis on chromosome X and I have seen some papers doing the same. Regarding point b, I haven't ran any gene burden testing so wouldn't have any group file as an input. I will look into it.
Comments
2 comments
Two ideas:
a. SAIGE might not be accustomed to be used for sex chromosomes.
b. It seems there is an issue with the formatting of the group file: https://github.com/weizhouUMICH/SAIGE/issues/56
Alexandra Lee ? , Anastazie Sedlakova ? thank you for helping with this thread!
Hello Ondrej,
Thank you so much for the help. I think it's a version issue. Most recent versions can run analysis on chromosome X and I have seen some papers doing the same. Regarding point b, I haven't ran any gene burden testing so wouldn't have any group file as an input. I will look into it.
Thank you so much.
Regards
Akhil
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