Closed noeri-mohamed-hoesein closed 9 months ago
@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!
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
Hi,
I tried to run
test_polyfun.py
, but I get the same recurring error message: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?