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molgenis / systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool

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"Error writing output data:Trying to write alleles" Issue?

wwhengold opened this issue · comments

commented

When running Genotypeharmonizer, I come across an error:
Input:
GenotypeHarmonizer.sh --input file --o file2 -r reference.file -R VCF

Output:
Writing results

Error writing output data: Trying to write alleles [G] for G\A SNP.

I've used GenotypeHarmonizer on previous chr without issue so far. Do you have suggestions on how exactly to find out more about this error? I wasn't able to find an answer in the documentation. Thank you very much

commented

Could you please share your log file. This should contain a bit more information on the error.

commented

FATAL - Error writing output data: Trying to write alleles [G] for G\A SNP
org.molgenis.genotype.GenotypeDataException: Trying to write alleles [G] for G\A SNP
at org.molgenis.genotype.plink.BedBimFamGenotypeWriter.writeBimBedFile(BedBimFamGenotypeWriter.java:178)
at org.molgenis.genotype.plink.BedBimFamGenotypeWriter.write(BedBimFamGenotypeWriter.java:74)
at org.molgenis.genotype.plink.BedBimFamGenotypeWriter.write(BedBimFamGenotypeWriter.java:55)
at nl.umcg.deelenp.genotypeharmonizer.GenotypeHarmonizer.main(GenotypeHarmonizer.java:421)

Do you need the entire log file or just this part?

commented

Thank you, I will have a look