Test_polyfun.py failed: extract_snpvar command failed

[noeri-mohamed-hoesein]

Hi,

I tried to run test_polyfun.py, but I get the same recurring error message:

Traceback (most recent call last):
  File "test_polyfun.py", line 304, in <module>
    test_extract_snpvar(temp_dir, args.python3)
  File "test_polyfun.py", line 210, in test_extract_snpvar
    raise ValueError('extract_snpvar command failed')
ValueError: extract_snpvar command failed

The python version that is used is 3.8.16

Looking at the error It's not really clear what's going wrong here. Can you help me out here?

[omerwe]

@noeri-mohamed-hoesein thanks for the feedback. I just updated the code to print out the exact command that failed. Can you please run git pull, rerun this, and then run the exact command that was reported to fail? Please respond with the error that you get when running that command. Thanks!

[noeri-mohamed-hoesein]

Okay so I did that. I ran the same command after git pull and got this:

Traceback (most recent call last):
  File "test_polyfun.py", line 309, in <module>
    test_extract_snpvar(temp_dir, args.python3)
  File "test_polyfun.py", line 215, in test_extract_snpvar
    raise ValueError('extract_snpvar command failed when running the following command:\n%s'%(cmd))
ValueError: extract_snpvar command failed when running the following command:
python /hpc/local/Rocky8/dhl_ec/software/polyfun/extract_snpvar.py --sumstats /hpc/local/Rocky8/dhl_ec/software/polyfun/example_data/snps_to_finemap.txt.gz --out /tmp/tmprisadsqs/snps_with_var.gz

So I ran the command, but I didn't get an error. Instead I got this output :

[INFO]  Loading sumstats files...
[INFO]  Done in 0.77 seconds
[INFO]  Loading meta-analyzed per-SNP-h2 files...
[INFO]  Done in 106.70 seconds
[INFO]  Merging sumstats with per-SNP h2 data...
[INFO]  Done in 3.34 seconds
[INFO]  Writing output file to /tmp/tmprisadsqs/snps_with_var.gz

But I don't know where exactly the output file is located and I couldn't figure that out as well by looking at the test_polyfun.py