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bvilhjal / ldpred

MIT License
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P+T #85

Closed bnj50 closed 4 years ago

bnj50 commented 5 years ago

The program somehow unable to read the P+T file LDpred1.py p+t --cf ref-psc1 --ldr 1000 --out pt --p 0.0001 1) a pt file being generated = pt_P+T_r0.20_p1.0000e-04.txt 2) change the file name above to just pt with the same prefix
LDpred1.py score --gf psc4 --rf pt --out pscprepPT --pf psc4.fam --pf-format FAM --rf-format P+T --pcs-file PCpsc.txt parsing phenotypes psc4.fam Parsed 1763 phenotypes successfully Traceback (most recent call last): File "/usr/local/ldpred/1.0.0/LDpred1.py", line 300, in main() File "/usr/local/ldpred/1.0.0/LDpred1.py", line 293, in main validate.main(p_dict) File "/usr/local/ldpred/1.0.0/ldpred1/validate.py", line 721, in main assert not prs_file_is_missing, 'No SNP weights file was found. A prefix to these should be provided via the --rf flag. Note that the prefix should exclude the LDpred.. extension or file ending. ' AssertionError: No SNP weights file was found. A prefix to these should be provided via the --rf flag. Note that the prefix should exclude the LDpred.. extension or file ending.

I am not using LDpred here but p+t option. appreciate your helps...

kovre commented 4 years ago

I have the exact same issue. Everything else works, but I am getting the "no SNP weights found" error when trying to generate a P+T score.

Edit: This issue appears to be (in my case at least) caused by defining a p value threshold when creating the P+T file. Try running it without defining the p value (assuming you did so before getting the error).

bvilhjal commented 4 years ago

Thanks for this error report. I believe I've fixed it now.

marine11 commented 3 years ago

Hello I have the same problem. I use v.1.0.10. Has it been resolved? Thank you.