symbol issue when importing weights

[quattro]

See here: bogdanlab/focus#50

[neurogenetics1]

Hi,
I have the same issue, and installing MA-FOCUS did not help solve it. Is there any update, or has a db for PrediXcan models been published yet?

Thanks

[DoraCChen]

Hi, I also wanted to check on this issue to see if there have been any updates.

[zeyunlu]

will only specifing "--from-gencode", instead of "--use-ens-id" solve the issue?

[DoraCChen]

Thanks for the help! I tried specifying only --from-gencode to prune off the transcript version and unfortunately am encountering the same issue:

focus import
/wittelab/data4/TWAS/PredictDB/mashr/eqtl/mashr_Prostate.db
predixcan
--tissue Prostate
--name GTEx
--assay rnaseq
--from-gencode
--output Prostate

Starting log...
[2024-03-20 14:11:41 - INFO] Preparing weight database
[2024-03-20 14:11:42 - INFO] Starting import from PrediXcan database /wittelab/data4/TWAS/PredictDB/mashr/eqtl/mashr_Prostate.db
[2024-03-20 14:11:44 - INFO] Querying mygene servers for gene annotations
[2024-03-20 14:12:15 - INFO] Starting individual model conversion
[2024-03-20 14:12:47 - INFO] Committed 250 models to db
[2024-03-20 14:13:05 - INFO] Committed 250 models to db
[2024-03-20 14:13:23 - INFO] Committed 250 models to db
[2024-03-20 14:13:42 - INFO] Committed 250 models to db
[2024-03-20 14:13:59 - INFO] Committed 250 models to db
[2024-03-20 14:14:16 - INFO] Committed 250 models to db
[2024-03-20 14:14:32 - INFO] Committed 250 models to db
[2024-03-20 14:14:42 - INFO] Committed 250 models to db
[2024-03-20 14:14:54 - INFO] Committed 250 models to db
[2024-03-20 14:15:07 - INFO] Committed 250 models to db
[2024-03-20 14:15:19 - INFO] Committed 250 models to db
[2024-03-20 14:15:33 - INFO] Committed 250 models to db
[2024-03-20 14:15:46 - INFO] Committed 250 models to db
[2024-03-20 14:15:58 - INFO] Committed 250 models to db
[2024-03-20 14:16:08 - INFO] Committed 250 models to db
[2024-03-20 14:16:16 - ERROR] 'symbol'
[2024-03-20 14:16:16 - INFO] Finished importing prediction models

In a previous thread, someone debugged and said that ENSG00000124593.15 seems to be the specific gene that's causing the error.