GDCprepare() error: 'I couldn't find all the files from the query. Please check if the directory parameter is right or GDCdownload downloaded the samples'

[maronem]

Hello,

I am having an issue preparing mutation and proteomics data from the TCGA-READ and COAD projects. I have used this same method for gene expression data which worked fine but for these queries and others using the same method I am running into this error each time.

Example query:
tcga_prot_query <- GDCquery(project = c('TCGA-READ', 'TCGA-COAD'),
data.category = 'Proteome Profiling',
data.type = 'Protein Expression Quantification')

tcga_prot_output <- getResults(tcga_prot_query)
tcga_prot_prep <- GDCprepare(tcga_prot_query, summarizedExperiment = TRUE)

Error:

Session info:

Thank you in advance for the help!