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genepi / imputationserver

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity
https://imputationserver.sph.umich.edu/
GNU Affero General Public License v3.0
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Imputation on chromosome 14 failed. Imputation was stopped. #72

Closed RichardB96 closed 2 years ago

RichardB96 commented 2 years ago

I am trying to impute a dataset aligned to the HRC reference panel on minimac4 using that same HRC panel, however every job I run gets to the prephasing/imputation phase and stops with the error:

Imputation on chromosome 14 failed. Imputation was stopped.

​There isn't any error files or much to try and diagnose this problem from my end - I am unsure if chr14 is the first to be imputed and this is indicative of issues with my dataset, or else they are imputed in order and there is just something wrong with chr14 etc. If this is something you've come across and/or you know what the problem could be it would be very helpful!

RichardB96 commented 2 years ago

error in data pre-processing, nothing server side

Fiwx commented 1 year ago

@RichardB96 what was the error in pre-processing?