Error loading the hg38 reference database and the hg38 covariate files

[gat2010]

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]

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