Question: Error via running GDCquey from TCGAbiolinks package
0
gravatar for modarzi
11 months ago by
modarzi10
modarzi10 wrote:

Hi,
I wanted to run below query via GDCquey:

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

#but I got below error:

Error in value[3L] :
GDC server down, try to use this package later

my sessioninfo() is :

R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

I appreciate if you share your comment with me.
Best Regards,
Mohammad

 

 

ADD COMMENTlink modified 11 months ago • written 11 months ago by modarzi10
1
"GDC server down, try to use this package later"

Try Now, the server is running!

ADD REPLYlink written 11 months ago by mario.zanfardino150

Hi,

Thanks for your comment. I tried now but unfortunately I received below message again:

Error in value[[3L]](cond) : 
  GDC server down, try to use this package later

I don't know what is my problem? my query has problem or package needs some update or GDC server really is done?

I appreciate if you share your comment with me.

Best Regards,

Mohammad

ADD REPLYlink written 11 months ago by modarzi10
1

GDC server is not down. On my pc your command run!

ADD REPLYlink written 11 months ago by mario.zanfardino150

but unfortunately for me give below error again:

Error in value[[3L]](cond) : 
  GDC server down, try to use this package later
ADD REPLYlink written 11 months ago by modarzi10
1

Try to run this command:

> GenomicDataCommons::status()
$commit
[1] "e9e20d6f97f2bf6dd3b3261e36ead57c56a4c7cc"

$data_release
[1] "Data Release 12.0 - June 13, 2018"

$status
[1] "OK"

$tag
[1] "1.14.1"

$version
[1] 1

What's your response?

 

ADD REPLYlink modified 11 months ago • written 11 months ago by mario.zanfardino150
1

I run this command and got these results:

> GenomicDataCommons::status()
$`commit`
[1] "e9e20d6f97f2bf6dd3b3261e36ead57c56a4c7cc"

$data_release
[1] "Data Release 12.0 - June 13, 2018"

$status
[1] "OK"

$tag
[1] "1.14.1"

$version
[1] 1
ADD REPLYlink modified 11 months ago • written 11 months ago by modarzi10
1

Try to reinstall TCGAbiolink with this command:

devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")
ADD REPLYlink modified 11 months ago • written 11 months ago by mario.zanfardino150

Thanks for your comment. I reinstalled it again and downloading was started based on below message:

> GDCdownload(query)

Downloading data for project TCGA-SARC
GDCdownload will download 259 files. A total of 131.671197 MB
Downloading as: Fri_Jun_29_15_08_52_2018.tar.gz

 

But after downloading 130 MB data I received below message for more than 20 times:

Downloading: 130 MB     <simpleWarning in file.create(to[okay]): cannot create file 'GDCdata/TCGA-SARC/harmonized/Transcriptome_Profiling/Gene_Expression_Quantification/c4b3ad46-a679-4ab8-9734-fed35846e691/e9d959e9-5e2d-4652-9ba4-4aeb1e7459be.FPKM-UQ.txt.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/9ec43d2a-bd49-434d-86a1-bd0cf7171dc2/d184d4f3-dc4e-4643-86b8-20dfaf6ee653.FPKM-UQ.txt.gz', reason 'No such file or directory'>

.

.

.

so when I wanted to run below code:

data <- GDCprepare(query, summarizedExperiment = FALSE)

system response me as below:

Error in GDCprepare(query, summarizedExperiment = FALSE) : 
  I couldn't find all the files from the query. Please check if the directory parameter right or GDCdownload downloaded the samples.

I think my download process has problem but i don't know what is it?

I appreciate if you share your comment with me.

ADD REPLYlink written 11 months ago by modarzi10
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