What does Ricoplili aspect of me

[42elenz]

First, thank you very much for the repo and the scripts provided.

I have a problem at the moment to figure out what exactly Ricopili expects as input for the imputation step and where and why it fails.
I’m trying to run the imputation pipeline, and I already have the following input files:
Example input files:
.bim file:
1 rs3094315 0 752566 C T
.fam file:
cas_alz_alz2_eur_EL_OMEX*1 137_S_4303 0 0 2 2

Even with --debug enabled, the error messages don’t clearly indicate what is wrong with the input format.
that is the error I get:

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Error:

step preph has been done repeatedly without any progress

imputation pipeline stopped: impute_dirsub --refdir /zi/home/esra.lenz/ricopili_refs/ --out adni --serial --sepa 10 --debug

home/user/Documents/01_LEARNING/RECOMPILI/00_datasets/00_ADNI/ADNI_2/ADNI2_hg38/qc/imputation impute_dirsub --refdir home/user/ricopili_refs/ --out adni --serial --sepa 10 --debug

if reason does not appear obvious

have a look at the wiki page

https://sites.google.com/a/broadinstitute.org/ricopili/

or contact the developers

version: 2025_Jan_30.003

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Do you have any ideas what could be the problem and what usually fails at this step?
I am trying to debug this now for several hours but just can not find the right combination of inputs :/

I hope that you can help there :)