Error: Import weights from predixcan and fusion

[gpwhiz]

Hi!
I am trying to import weights from predixcan and fusion and I get an error for each method.
I have the following versions of
pandas 1.3.5
pandas-plink 2.2.9

Error in predixcan

focus import
       path/eqtl/mashr/mashr_Brain_Cerebellar_Hemisphere.db
        predixcan
        --tissue brain_cereb_hemisphere
        --name predix.gtexv8
        --assay rnaseq
        --output predix_cereb_hemisphere.db

Starting log...
[2023-09-05 19:24:03 - INFO] Preparing weight database
[2023-09-05 19:24:04 - INFO] Starting import from PrediXcan database path/eqtl/mashr/mashr_Brain_Cerebellar_Hemisphere.db
INFO:MAIN:Starting import from PrediXcan database path/eqtl/mashr/mashr_Brain_Cerebellar_Hemisphere.db
[2023-09-05 19:24:04 - ERROR] __init__() got multiple values for argument 'schema'
ERROR:MAIN:__init__() got multiple values for argument 'schema'
[2023-09-05 19:24:04 - INFO] Finished importing prediction models

Error in fusion

===================================
             FOCUS v0.802
===================================
focus import
        path/fusion_twas-master/CMC.BRAIN.RNASEQ/CMC.BRAIN.RNASEQ.pos
        fusion
        --tissue brain_dorsolateral_prefrontal_cortex
        --name cmc
        --assay rnaseq
        --output fusion.cmc

Starting log...
[2023-09-05 19:14:02 - INFO] Preparing weight database
INFO:rpy2.situation:cffi mode is CFFI_MODE.ANY
INFO:rpy2.situation:R home found: /conda_envs/focus/lib/R
INFO:rpy2.situation:R library path:/conda_envs/focus/lib/python3.7/site-packages/cv2/../../lib64:
INFO:rpy2.situation:LD_LIBRARY_PATH: /conda_envs/focus/lib/python3.7/site-packages/cv2/../../lib64
INFO:rpy2.rinterface_lib.embedded:Default options to initialize R: rpy2, --quiet, --no-save
INFO:rpy2.rinterface_lib.embedded:R is already initialized. No need to initialize.
[2023-09-05 19:14:05 - INFO] Starting import from FUSION database path/fusion/fusion_twas-master/CMC.BRAIN.RNASEQ/CMC.BRAIN.RNASEQ.pos
INFO:MAIN:Starting import from FUSION database /path/fusion/fusion_twas-master/CMC.BRAIN.RNASEQ/CMC.BRAIN.RNASEQ.pos
[2023-09-05 19:14:05 - INFO] Querying mygene servers for gene annotations
INFO:MAIN:Querying mygene servers for gene annotations
[2023-09-05 19:14:18 - INFO] Starting individual model conversion
INFO:MAIN:Starting individual model conversion
[2023-09-05 19:14:18 - ERROR] 'Series' object has no attribute 'DIR'
ERROR:MAIN:'Series' object has no attribute 'DIR'
[2023-09-05 19:14:18 - INFO] Finished importing prediction models
INFO:MAIN:Finished importing prediction models

Any advice would be much appreciated?

[elnetwas]

Hello, I'm new to using Focus for fine mapping, and I'm encountering the same issue. Did you manage to solve it in the end?

[zeyunlu]

hi, has this issue been solved? It would be great if you can add --verbose to the command.