File "postgap_main.py", line 702, in <module>

[jielab]

Dear Daniel:

Happy New Year!

After I renamed the folder postgap to postgap_master, and also renamed POSTGAP.py to postgap_main.py, the previous error message of "No module named GWAS" went away. I am using the Ubuntu linux coming with Windows 10. Maybe there is some issue with the uppercase and lowercase of file names.

Please see the screenshot below. I now got a different error message.

Can you please let me know how to resolve this?

Thank you & Best regards,
Jie

[dzerbino]

Hello @jielab ,

Happy New Year to you too!

Evidently it is not finding the 1000 genomes vcf files under the databases directory provided in the command line.

Did you download all the data files as explained in the README?

Cheers,

Daniel

[jielab]

Thanks, Daniel!

Please see the attached screenshot below. The "1000Genomes" folder is there.

The above command has been running for a few hours already. There is no error message, but no output either.

Best regards,
Jie

[dzerbino]

Hello Jie,

It's probably taking its time, autism probably has a ton of GWAS hits in the GWAS Catalog.

Cheers,

Daniel

[jielab]

Dear Daniel:

I happen to know Autism GWAS research. Compared with a lot of complex traits, there are only few published GWAS for Autism.

My command stayed unchanged for more than 18 hours. I wish there is a way to check the progress if the program is actually working on something. Anyway, I had to kill the job.

I changed to a different test command, as shown below. This time, I got an error message right away. So, it seems there is still some issue with the program that I installed.

Best regadrs,
jie

[dzerbino]

Hello @jielab,

Thank you for the update. Did you install the dependencies, as per the README? Were there any error messages?

Cheers,

Daniel

[jielab]

Dear Daniel:

I did install the dependencies, following the README. However, the above error message still remains.

Best regards,
Jie