Problem for downloading data from Genomic Data Commons portal via TCGAbiolinks package
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modarzi ▴ 10
@modarzi-16296
Last seen 7 months ago

Hi,
I wanted to run below query via GDCquey:

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

but I got below error:

Downloading: 500 kB <simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-SARC/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'>
<simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-SARC/harmonized/Transcriptome_Profiling/Gene_Expression_Quantification/e2054010-5b2d-4072-84c7-687cafecd16f/37a13940-09d8-4a6f-95fe-83fa0bc0b6c2.htseq.counts.gz', reason 'No such file or directory'>

I appreciate if anybody share his/her comment with me.
Best Regards,
Mohammad

TCGAbiolinks RNA-seq • 388 views
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tiagochst ▴ 150
@tiagochst-7121
Last seen 23 months ago
Brazil

That's a windows problem. Paths have a limit of 260 long path in windows. But it seems to be hackable in windows 10 (https://lifehacker.com/windows-10-allows-file-names-longer-than-260-characters-1785201032)

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Hi @tiagochst

Thanks for your comment. I appreciate if you help me for doing what action for solving my problem.

Best Regards,

Mohammad

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