Question: Error via running GDCdownload() in TCGAbiolinks
gravatar for modarzi
8 months ago by
modarzi10 wrote:


I provide below query:

query <- GDCquery(project = "TCGA-SARC",sample.type = "Primary solid Tumor",
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification",workflow.type = "HTSeq - FPKM-UQ");

after that for downloading my data, I run below code:

GDCdownload(query, method= "api", directory = "mydata")

So I tried the GDCdownloads, it starts downloading, but it gives me an error saying the file or directory does not exist:

"<simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-SKCM/harmonized/Transcriptome_Profiling/Gene_Expression_Quantification/3c9fe8ef-e394-4d7a-9189-de6ce2169c45/50bbf24f-b914-4e53-98ee-0cf22b2d9f01.htseq.counts.gz', reason 'No such file or directory'>

I appreciate if anybody share his/ her comment with me.

Best Regards,

download tcga tcgabiolinks • 183 views
ADD COMMENTlink modified 8 months ago by Tiago Chedraoui Silva240 • written 8 months ago by modarzi10
Answer: Error via running GDCdownload() in TCGAbiolinks
gravatar for Tiago Chedraoui Silva
8 months ago by
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Tiago Chedraoui Silva240 wrote:


I ran a small example and it worked. Probably the folder was not created in the system. If it is a windows OS, there is a limit of characters in the full path (I believe it is 256 characters), you might be able to check the path length it is trying to create with:


Best regards, Tiago Chedraoui Silva

ADD COMMENTlink written 8 months ago by Tiago Chedraoui Silva240


My OS is windows 10. when I run getwd() I see below path:

"E:/Biology_base/RNA-seq/GDC-TCGA-SARC/Original_data/SARC RNA-seq by TCGAbiolink Package-971215"

so when I run below code:


in "SARC RNA-seq by TCGAbiolink Package-971215" folder I see new folder by "GDCdata" and below path:


but in "0b4a4b61-ce8e-4fda-b0ee-4cc6ec3e2474" folder I can't find any file. Also I call stringr library but in that I couldn't find strlength(). I fould str_length()

So I request to help me and give your solution based on my explanation . Best Regards

ADD REPLYlink written 8 months ago by modarzi10

The package is trying to create a file that has 267 characters (considering the full path) which more than the limit of 260 characters. You should either enable long paths (, or reduce the name of same folders or work in the upper directories

like working inside this path: "E:/Biologybase/RNA-seq/GDC-TCGA-SARC/Originaldata/"

ADD REPLYlink written 8 months ago by Tiago Chedraoui Silva240
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