Question: Problem for downloading data from Genomic Data Commons portal via TCGAbiolinks package
0
gravatar for modarzi
16 months ago by
modarzi10
modarzi10 wrote:

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

rna-seq tcgabiolinks • 268 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by modarzi10
Answer: C: Problem for downloading data from Genomic Data Commons portal via TCGAbiolinks p
1
gravatar for tiagochst
16 months ago by
tiagochst150
Brazil
tiagochst150 wrote:

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)

ADD COMMENTlink written 16 months ago by tiagochst150

Hi @tiagochst

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

Best Regards,

Mohammad

ADD REPLYlink written 16 months ago by modarzi10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 376 users visited in the last hour