[ERROR] 'symbol'

[Kris69w]

Hi I got an error when importing gtex v8 mashr model.

===================================
              FOCUS v0.6.10            
===================================
focus import
        mashr_Lung.db
        predixcan
        --tissue Lung
        --name GTEx
        --assay rnaseq
        --output mashr_lung_focus

Starting log...
[2020-11-05 07:06:59 - INFO] Preparing weight database
[2020-11-05 07:06:59 - INFO] Starting import from PrediXcan database mashr_Lung.db
[2020-11-05 07:06:59 - INFO] Querying mygene servers for gene annotations
[2020-11-05 07:16:43 - INFO] Starting individual model conversion
[2020-11-05 07:16:43 - ERROR] 'symbol'
[2020-11-05 07:16:43 - INFO] Finished importing prediction models

Not sure what it means. any help is appreciated.

[BinglanLi]

Along the same line, I tried to generate GTEx v8 elastic net-based eQTL models and used '--use-ens-id' flag. I got the same error.

[quattro]

The code on the dev branch should be able to work in this setting. I will aim to push to master branch early this year with some other changes.

[pmk2020]

I am receiving the same error. I am using the mashr GTEx v8 models to create weights

[WeiCSong]

Hi, seems that dev branch still contains some error. I downloaded dev branch and installed with setup.py, and met the following error:

===================================

        FOCUS v0.7             

===================================
focus import
mashr_Liver.db
predixcan
--tissue Liver
--name GTEx
--assay rnaseq
--output gtex_v8

Starting log...
[2021-05-17 10:56:08 - INFO] Preparing weight database
[2021-05-17 10:56:13 - INFO] Starting import from PrediXcan database mashr_Liver.db
[2021-05-17 10:56:13 - INFO] Querying mygene servers for gene annotations
[2021-05-17 10:56:59 - INFO] Starting individual model conversion
[2021-05-17 10:57:12 - INFO] Committed 250 models to db
[2021-05-17 10:57:24 - INFO] Committed 250 models to db
[2021-05-17 10:57:37 - INFO] Committed 250 models to db
[2021-05-17 10:57:50 - INFO] Committed 250 models to db
[2021-05-17 10:58:03 - INFO] Committed 250 models to db
[2021-05-17 10:58:16 - INFO] Committed 250 models to db
[2021-05-17 10:58:31 - INFO] Committed 250 models to db
[2021-05-17 10:58:46 - INFO] Committed 250 models to db
[2021-05-17 10:58:59 - INFO] Committed 250 models to db
[2021-05-17 10:59:12 - INFO] Committed 250 models to db
[2021-05-17 10:59:26 - INFO] Committed 250 models to db
[2021-05-17 10:59:41 - INFO] Committed 250 models to db
[2021-05-17 10:59:56 - INFO] Committed 250 models to db
[2021-05-17 11:00:11 - INFO] Committed 250 models to db
[2021-05-17 11:00:21 - ERROR] 'symbol'
[2021-05-17 11:00:21 - INFO] Finished importing prediction models

I guess the number of models is surely larger than this, so there should be something wrong before the completion of import.

EDIT:

BTW, after running debug mode, I found it was ENSG00000124593.15 that caused the error. I search for this gene and found that it has the symbol RP11-298J23 in gtex data.

[funfunchen]

looks like the symbol error is still there?
btw, I tried the gtex.v7 data
thanks.

[neurogenetics1]

I have the same error. Has anyone figured out how to correct it?