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Issue when downloading DNA methylation data with GDCdownload #642

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DanielJMullen opened this issue Feb 28, 2025 · 0 comments
Open

Issue when downloading DNA methylation data with GDCdownload #642

DanielJMullen opened this issue Feb 28, 2025 · 0 comments

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@DanielJMullen
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I'm not sure if this is due to a temporary outage with the GDC's servers, but I have been encountering the error "Downloading: 350 MB dcfe1340-4c0a-427c-9fb8-a3cecd8775f0/2ab8eb6b-f68d-4a7a-b9ba-9073633b8d38.methylation_array.sesame.level3betas.txt: Truncated tar archive detected while reading data: Unknown error tar.exe: Error exit delayed from previous errors." when I try downloading DNA methylation data (there seems to be no error when downloading expression data).

These are the commands I've been running:

methylationQuery <- TCGAbiolinks::GDCquery(
project ="TCGA-BRCA",
data.category = "DNA Methylation",
data.type = "Methylation Beta Value",
platform = "Illumina Human Methylation 450"
)

TCGAbiolinks::GDCdownload(
methylationQuery,
directory = "path/on/local/machine"
)

Whereas these worked for expression data:

expressionQuery <- TCGAbiolinks::GDCquery(
project = "TCGA-BRCA",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
experimental.strategy = "RNA-Seq",
workflow.type = "STAR - Counts"
)

TCGAbiolinks::GDCdownload(
expressionQuery,
directory = "path/on/local/machine"
)

Thank you for any advice you have with this issue!

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