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kauwelab / PolyRiskScore

PRSKB is a website and command-line interface tool for calculating polygenic risk scores using GWA studies from the NHGRI-EBI Catalog.
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ERROR DURING CALCULATION... Quitting - While using PolyRiskScore/static/sample.vcf #430

Closed alisondiazc closed 8 months ago

alisondiazc commented 1 year ago

Greetings to the creators of PRSKB tool. I am trying to perform a test with the provided VCF file at PolyRiskScore/static/sample.vcf, and I encountered the error "ERROR DURING CALCULATION... Quitting," which seems to be caused by errors during the execution of the script parse_associations.py. Could you guide me on what could be causing this error? Alternatively, could you provide a sample file that allows me to observe the correct functioning of the tool, so that I can then adapt my input VCF?

The command I am using is "./runPrsCLI.sh -f /root/PRSKB/sample.1.vcf -o /root/PRSKB/sample.1.PRS.json -c 0.05 -r hg38 -p AMR." The version I am using is "1.9.0."

mpage21 commented 1 year ago

Hi @alisondiazc,

You say that the errors seem to come from the parse_associations.py script. Were there additional error messages that led to you to that conclusion? If you could add them here, that would be very helpful.

mpage21 commented 11 months ago

@alisondiazc just checking back to see if you could post the error messages. Otherwise, in August we will close this issue.