Question

Error via running GDCdownload() in TCGAbiolinks

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modarzi ▴ 10

@modarzi-16296

Last seen 3.5 years ago

Hi,

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,

TCGAbiolinks TCGA Download • 2.0k views

ADD COMMENT • link updated 5.2 years ago by Tiago Chedraoui Silva ▴ 260 • written 5.2 years ago by modarzi ▴ 10

score 0 · Answer 1 · 2019-03-06

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Tiago Chedraoui Silva ▴ 260

@tiago-chedraoui-silva-8877

Last seen 3.7 years ago

Brazil - University of São Paulo/ Los A…

Hello,

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:

stringr::strlength(file.path(getwd(),"GDCdata/TCGA-SKCM/harmonized/TranscriptomeProfiling/GeneExpressionQuantification/3c9fe8ef-e394-4d7a-9189-de6ce2169c45/50bbf24f-b914-4e53-98ee-0cf22b2d9f01.htseq.counts.gz"))

Best regards, Tiago Chedraoui Silva

ADD COMMENT • link 5.2 years ago Tiago Chedraoui Silva ▴ 260

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Hi,

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:

GDCdownload(query)

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

GDCdata\TCGA-SARC\harmonized\Transcriptome_Profiling\Gene_Expression_Quantification\0b4a4b61-ce8e-4fda-b0ee-4cc6ec3e2474

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 REPLY • link 5.2 years ago modarzi ▴ 10

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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 ( https://www.howtogeek.com/266621/how-to-make-windows-10-accept-file-paths-over-260-characters/), 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 REPLY • link 5.2 years ago Tiago Chedraoui Silva ▴ 260