Comments (5)
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.
from focus.
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.
from focus.
I am receiving the same error. I am using the mashr GTEx v8 models to create weights
from focus.
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_v8Starting 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.
from focus.
looks like the symbol
error is still there?
btw, I tried the gtex.v7 data
thanks.
from focus.
Related Issues (20)
- How to evaluate result of a gene in 2 region.
- Default --n-min in munge HOT 2
- FOCUS stalls on chromosome 6 HOT 3
- Importing weights from FUSION HOT 2
- Tissue prioritization HOT 1
- Cleaning GWAS summary data HOT 1
- Data folder doesn't contain gencode_map_v37.tsv HOT 8
- [ERROR] import_fusion 'Series' object has no attribute 'DIR' HOT 7
- unsupported operand type(s) for +: 'float' and 'str'
- [ERROR] Import submodule requires mygene and rpy2 to be installed
- [ERROR] ufunc 'isfinite' not supported for the input types HOT 2
- Please specify independent regions location or default regions with '37:EUR', etc HOT 2
- Integer column has NA values in column 3 HOT 4
- unsupported operand type(s) for +: 'float' and 'str' HOT 3
- Focus import error - "500 Server Error: Internal Server Error for url: http://mygene.info/v3/query/" HOT 2
- ERROR] MetaData.__init__() got multiple values for argument 'schema' HOT 1
- error in creating the weight database HOT 3
- symbol issue when creating weight database using Predixcan databases HOT 5
- name 'zscores' is not defined errror with when running finemap with --intercept HOT 2
- The TWAS z-score obtained by S-PrediXcan and FOCUS software is different
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