metaXcan Error

[Lanj]

Hello, 

I am new to MetaXcan. I followed the instructions to download and extract the program to my local directory. I tried to run the example using the exact same command described on the website and I got error message. I am not sure what's wrong and I hope someone here can help me figure out. Thank you!

 ./MetaXcan.py --model_db_path data/DGN-WB_0.5.db --covariance data/covariance.DGN-WB_0.5.txt.gz --gwas_folder data/GWAS --gwas_file_pattern ".*gz" --snp_column SNP --effect_allele_column A1 --non_effect_allele_column A2 --beta_column BETA --pvalue_column P --output_file results/test.csv

Traceback (most recent call last):

  File "./MetaXcan.py", line 12, in <module>

    from metax.gwas import Utilities as GWASUtilities

  File "MetaXcan/software/metax/gwas/Utilities.py", line 7, in <module>

    import GWAS

ModuleNotFoundError: No module named 'GWAS'

[Alvaro Barbeira]

Hi there,

Which version of python are you using? i.e. would you be able to post the output of executing python --version on a terminal?

Best,

Alvaro

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[Lanj]

I am using Python 2.7.12. Thanks!

On Tuesday, June 12, 2018 at 5:04:37 PM UTC-7, Alvaro Barbeira wrote:

Hi there,

Which version of python are you using? i.e. would you be able to post the output of executing python --version on a terminal?

Best,

Alvaro

On Tue, Jun 12, 2018 at 5:26 PM, Lanj <lanj...@gmail.com> wrote:

Hello, 

I am new to MetaXcan. I followed the instructions to download and extract the program to my local directory. I tried to run the example using the exact same command described on the website and I got error message. I am not sure what's wrong and I hope someone here can help me figure out. Thank you!

 ./MetaXcan.py --model_db_path data/DGN-WB_0.5.db --covariance data/covariance.DGN-WB_0.5.txt.gz --gwas_folder data/GWAS --gwas_file_pattern ".*gz" --snp_column SNP --effect_allele_column A1 --non_effect_allele_column A2 --beta_column BETA --pvalue_column P --output_file results/test.csv

Traceback (most recent call last):

  File "./MetaXcan.py", line 12, in <module>

    from metax.gwas import Utilities as GWASUtilities

  File "MetaXcan/software/metax/gwas/Utilities.py", line 7, in <module>

    import GWAS

ModuleNotFoundError: No module named 'GWAS'

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[Lanj]

I think I know what's wrong. I didn't install all the necessary python packages. Thank you for your reply!

On Tuesday, June 12, 2018 at 5:04:37 PM UTC-7, Alvaro Barbeira wrote:

Hi there,

Which version of python are you using? i.e. would you be able to post the output of executing python --version on a terminal?

Best,

Alvaro

On Tue, Jun 12, 2018 at 5:26 PM, Lanj <lanj...@gmail.com> wrote:

Hello, 

I am new to MetaXcan. I followed the instructions to download and extract the program to my local directory. I tried to run the example using the exact same command described on the website and I got error message. I am not sure what's wrong and I hope someone here can help me figure out. Thank you!

 ./MetaXcan.py --model_db_path data/DGN-WB_0.5.db --covariance data/covariance.DGN-WB_0.5.txt.gz --gwas_folder data/GWAS --gwas_file_pattern ".*gz" --snp_column SNP --effect_allele_column A1 --non_effect_allele_column A2 --beta_column BETA --pvalue_column P --output_file results/test.csv

Traceback (most recent call last):

  File "./MetaXcan.py", line 12, in <module>

    from metax.gwas import Utilities as GWASUtilities

  File "MetaXcan/software/metax/gwas/Utilities.py", line 7, in <module>

    import GWAS

ModuleNotFoundError: No module named 'GWAS'

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[Pingüín Norimaki]

I have the same problem...

[Tang Yaling]

May I ask which packages you did not install ? Thanks.

I followed all the instructions required on the website but still got the same error. 

在 2018年6月14日星期四 UTC-4下午5:38:23，Lanj写道：

[Alvaro Barbeira]

Hi Tang,

This error typically arises when using a python version other than 2.7. All other python versions are unsupported at the moment.

The current list of dependencies is:

scipy>=1.2.2,<1.3

numpy>=1.14.2

pandas>=0.22.0

mock>=2.0.0

patsy>=0.5.0

statsmodels>=0.10.0

h5py>=2.7.1

h5py-cache>=1.0

Only the first three are needed for S-PrediXcan (MetaXcan.py), the rest are needed for MultiXcan.

Best,

Alvaro

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