Closed openpaul closed 8 months ago
Thanks @openpaul, making this check (and all the errors/assertions) more informative & robust is very much on our radar! Quick question: where you running the matching software with a single PGS consisting of a single variant?
cheers, its already and amazing resource you are building here. I am just learning how to work with snp data, so might have been my input data.
I was not using it though with a single PGS with a single variant. Cant find logs for it anymore, but will update you with the command I ran if I see the bug again.
I think it was triggered as my vcf file was too short, to few variants. But not sure
While learning how to use https://github.com/PGScatalog/pgsc_calc/ I came across the error:
Thrown by https://github.com/PGScatalog/pgscatalog_utils/blob/main/pgscatalog_utils/match/combine_matches.py#L52
In my case I debugged the input file and found that
Clearly the issue is not duplicated IDs but rather no ids. I added a small debug statement and got:
I am not sure what check to add or how such a situation should be handled, but currently the
pgsc_calc
just crashed quite harshly.This is related to https://github.com/PGScatalog/pgsc_calc/issues/72 and https://github.com/PGScatalog/pgscatalog_utils/issues/36.
I hope this helps making the pipeline more robust.