GDCPrepare error (No such process)
1
0
Entering edit mode
8 weeks ago
aUser ▴ 30

Hi,

I am trying to do mutation analysis from TCGA data, and I am doing it using a simple process like this:

query.met <- GDCquery(
project = project,
data.category = "Simple Nucleotide Variation",
access = "open",
data.type = "Masked Somatic Mutation",
workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking")

mut <- GDCprepare(query.met)


But, it is giving me an error as:

Error: No such process.


I tried TCGA-LUAD, TCGA-LUSC, and TCGA-COAD as projects, but the error is the same in all cases.

I tried googling but did not get any clue. If anybody could point out any error or hint, that would be great.

TCGABiolinks GDCPrepare • 261 views
1
Entering edit mode
8 weeks ago
aUser ▴ 30

Just restarting the R session fixed the problems. It may be due to pending updates (the already loaded libraries do not update) or any other unknown error that was not visible/discernable from this error. I don't want to restart the session that was the reason I was looking for some help.