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Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
GNU General Public License v3.0
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Custom annotation option command not found #132

Open pablosolar opened 1 month ago

pablosolar commented 1 month ago

Hi!

I am running this command:

dotnet /home/Nirvana/bin/Release/net6.0/Nirvana.dll -c Cache/GRCh37/Both --sd SupplementaryAnnotation/GRCh37 -r Homo_sapiens.GRCh37.Nirvana.dat -i NA12878.chr1.9009406.vcf -o out/NA12878_nirvana --sd custom

where custom is an s3 directory with the following:

aws s3 ls s3://....nirvana/data/custom/            
2024-05-28 10:58:14        149 custom.nsa
2024-05-28 10:58:15         64 custom.nsa.idx
2024-05-28 10:58:15        450 custom.nsa.schema

but raising:

Some problems were encountered when parsing the command line options:
  - ERROR: Found unknown command-line option(s): --sd custom

Do you know what could be happening? If I remove the --sd custom, it works fine. Thanks!