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im3sanger / dndscv

dN/dS methods to quantify selection in cancer and somatic evolution
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Error loading the hg38 reference database and the hg38 covariate files #94

Open gat2010 opened 9 months ago

gat2010 commented 9 months ago

Hi,

I am getting the below errors while loading the hg38 reference database and the hg38 covariate files

load("Exome/covariates_hg19_hg38_epigenome_pcawg.rda")

Error in load("Exome/covariates_hg19_hg38_epigenome_pcawg.rda") : bad restore file magic number (file may be corrupted) -- no data loaded In addition: Warning message: file ‘covariates_hg19_hg38_epigenome_pcawg.rda’ has magic number '' Use of save versions prior to 2 is deprecated

A similar error while running the dndscv command without covariates

t <- dndscv(mut, refdb = "Exome/RefCDS_human_GRCh38_GencodeV18_recommended.rda", cv = NULL)

[1] Loading the environment... Error in load(refdb) : bad restore file magic number (file may be corrupted) -- no data loaded In addition: Warning message: file ‘RefCDS_human_GRCh38_GencodeV18_recommended.rda’ has magic number '' Use of save versions prior to 2 is deprecated

Kindly help in resolving the error.

Regards

Gaurav

im3sanger commented 7 months ago

Dear Gaurav,

Thank you for raising this issue and sorry for the late reply.

Are you still experiencing this problem? I am afraid I have never experienced it and cannot reproduce it. Can you try to download the file again? If this does not work, could you try to use load("Exome/RefCDS_human_GRCh38_GencodeV18_recommended.rda") and input the RefCDS object into dndscv using the refdb argument?

Best wishes, Inigo