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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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Data for REMM is not configured #538

Closed HongyuanChu closed 3 months ago

HongyuanChu commented 5 months ago

1707126329954 This appeared while performing "java -Xmx6g -jar ~/exomiser-cli-13.3.0/exomiser-cli-13.3.0.jar --analysis examples/NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38.yml --spring.config.location=/data/chuhy/exomiser-cli-13.3.0/application.properties --assembly hg38" The application.properties is as follows

exomiser.data-directory=data

exomiser.data-directory=/data/chuhy/exomiser-cli-13.3.0/data exomiser.hg19.data-version=2309 exomiser.hg38.data-version=2309 exomiser.hg19.variant-white-list-path=2309_hg19_clinvar_whitelist.tsv.gz exomiser.hg38.variant-white-list-path=2309_hg38_clinvar_whitelist.tsv.gz exomiser.phenotype.data-version=2309 exomiser.hg38.remm-path=ReMM.v0.4.hg38.tsv.gz

lpsyy commented 3 months ago

I think you should put the full path of the remm in the application properties, for example mnt/f/exomiser/exomiser-cli-13.3.0/data/2309_hg38/remm........

julesjacobsen commented 3 months ago

@HongyuanChu, as @Ipsyy said, you need to use the full path to the ReMM.v0.4.hg38.tsv.gz file.