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