run fine on one ancestry but has issue on two ancestries

[arkyl]

Hi,
Thanks much for the ma-focus software!
We have successfully run focus on one ancestry using our QTL data and public gwas. However, we had issues when we tried to run ma-focus on two ancestries (EUR/AFR). Even when we lower the --p-threshold to 1e-03, the output is empty for all chrs.
The main message from the log is "Aligning GWAS, LD, and eQTL weights .... No common genes found at region ..."; and "No common genes" for all regions. This is quite strange, as we had results on each individual ancestry by focus, and nearly 200 genes are in both results. So I assume ma-focus should run on many of them.
We further test on more gwas of more significant signals or larger sample size, and results are the same. The output is empty. So I think the issue is probably not from gwas itself.
I am wondering if you have experience like this before. Any advice on this issue is greatly appreciated!

Best,
Yue

[zeyunlu]

Hello, sorry about the late reply as I do not normally check the issue thread.

Did you resolve this issue? It would be great if you could send me the log with verbose turned on to my email so that I can take a further look.

See here for the relevant codes, it seems that your one of the ["ens_gene_id", "model_id", "ref_name"] does't match across not only the GWAS data but also eQTL weights data and LD reference data.