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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Downloading issue for project TCGA-GBM #519

Closed snashraf closed 1 year ago

snashraf commented 2 years ago

Dear Team,

I am trying to downloading count data for all TCGA cancer but it seems TCGA-GBM is not getting downloaded. I am getting the same error every time. Could you please fix this issue. 

i="TCGA-GBM"
 query.exp <- GDCquery(project = i, 
                          data.category = "Transcriptome Profiling", 
                          data.type = "Gene Expression Quantification", 
                          workflow.type = "STAR - Counts",
                          sample.type = c("Primary Tumor","Solid Tissue Normal"))
                      GDCdownload(query.exp, method = "api", files.per.chunk = 40)
                      print (paste0(i,".rda"))
                      GDCprepare(query = query.exp, save = TRUE, save.filename=paste0(i,".rda"))

Downloading data for project TCGA-GBM Of the 161 files for download 160 already exist. We will download only those that are missing ones. GDCdownload will download: 4.22931 MB Downloading chunk 1 of 1 (1 files, size = 4.22931 MB) as 64d208b9-6a15-4077-885f-30d9cdedf147.rna_seq.augmented__0.tar_gene_counts.tsv |======================================================================================================================| 100% At least one of the chunks download was not correct. We will retry Downloading chunk 1 of 1 (1 files, size = 4.22931 MB) as 64d208b9-6a15-4077-885f-30d9cdedf147.rna_seq.augmented__0.tar_gene_counts.tsv |======================================================================================================================| 100% ERROR : There was an error in the download process (we might had a connection problem with GDC server). Please run this function it again. Try using method = client or setting files.per.chunk to a small number.

tiagochst commented 2 years ago

@snashraf Thanks for pointing out this problem. It should be fixed now.

snashraf commented 2 years ago

I am still getting the same issue !!

tiagochst commented 2 years ago

@snashraf Just to be sure, do you have version 2.25.1 installed?

snashraf commented 2 years ago

Its TCGAbiolinks_2.25.0.

tiagochst commented 2 years ago

Please, update from github

BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")
BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")
snashraf commented 2 years ago

Hi ,

Now I have issue with downloading LAML . Could you please check this issue?

--------------------------------------
o GDCquery: Searching in GDC database
 --------------------------------------
 Genome of reference: hg38
 --------------------------------------------
 oo Accessing GDC. This might take a while...
 --------------------------------------------
ooo Project: TCGA-LAML
Sorry! There is no result for your query. Please check in GDC the data available or if there is no error in your query.
tiagochst commented 2 years ago

Could you post the query code you used please?

On Fri, Aug 5, 2022, 10:14 AM Najeeb Ashraf Syed @.***> wrote:

Hi ,

Now I have issue with downloading LAML . Could you please check this issue?

o GDCquery: Searching in GDC database Genome of reference: hg38 oo Accessing GDC. This might take a while...

ooo Project: TCGA-LAML Sorry! There is no result for your query. Please check in GDC the data available or if there is no error in your query.

— Reply to this email directly, view it on GitHub https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/519#issuecomment-1206446896, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDQ6LUKXWBIMQAJGSYQA3VXUHUDANCNFSM5YFUNWFA . You are receiving this because you commented.Message ID: @.***>

snashraf commented 2 years ago

i="TCGA-LAML" query.exp <- GDCquery(project = i , data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "STAR - Counts", sample.type = c("Primary Tumor","Solid Tissue Normal")) GDCdownload(query.exp, method = "api", files.per.chunk = 40)

tiagochst commented 2 years ago

@snashraf For TCGA-LAML the only option is Primary Blood Derived Cancer - Peripheral Blood

query.exp <- GDCquery(
    project = "TCGA-LAML",
    data.category = "Transcriptome Profiling",
    data.type = "Gene Expression Quantification",
    workflow.type = "STAR - Counts"
)
Screen Shot 2022-08-05 at 10 27 27 AM
snashraf commented 2 years ago

Thanks Tiago !

On Fri, Aug 5, 2022 at 4:28 PM Tiago Chedraoui Silva < @.***> wrote:

@snashraf https://github.com/snashraf For TCGA-LAML the only option is Primary Blood Derived Cancer - Peripheral Blood

query.exp <- GDCquery( project = "TCGA-LAML", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "STAR - Counts" )

[image: Screen Shot 2022-08-05 at 10 27 27 AM] https://user-images.githubusercontent.com/145529/183087142-962f1260-cc85-45e2-94aa-ede61ba7aaa2.png

— Reply to this email directly, view it on GitHub https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/519#issuecomment-1206459818, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBFIN62YQLR4NRZ7MZ5MCDVXUJH7ANCNFSM5YFUNWFA . You are receiving this because you were mentioned.Message ID: @.***>

-- Dr. Najeeb Ashraf Syed, Ph.D., M.tech, M.Sc (Bioinformatics) Google Scholar https://scholar.google.com/citations?user=YCzq27MAAAAJ&hl=en&oi=ao