GDCquery error downloading TARGET-AML data

Question

[Beth]

Hello there,

I'm trying to download TARGET-AML data via GDCquery:

library(TCGAbiolinks)
query_target <- GDCquery(project = "TARGET-AML",
                         data.category = "Transcriptome Profiling",
                         data.type = "Gene Expression Quantification",
                         workflow.type = "STAR - Counts")

And I got this error:

Warning messages:
1: In open.connection(con, "rb") :
  URL 'https://api.gdc.cancer.gov/files/?pretty=true&expand=cases,cases.samples.portions.analytes.aliquots,cases.project,center,analysis,cases.samples&size=10246&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TARGET-AML%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22STAR%20-%20Counts%22]%7D%7D]%7D&format=JSON': Timeout of 60 seconds was reached
2: In open.connection(con, "rb") :
  URL 'https://api.gdc.cancer.gov/files/?pretty=true&expand=cases,cases.samples.portions.analytes.aliquots,cases.project,center,analysis,cases.samples&size=10246&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TARGET-AML%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22STAR%20-%20Counts%22]%7D%7D]%7D&format=JSON': Timeout of 60 seconds was reached
3: In open.connection(con, "rb") :
  URL 'https://api.gdc.cancer.gov/files/?pretty=true&expand=cases,cases.samples.portions.analytes.aliquots,cases.project,center,analysis,cases.samples&size=10246&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TARGET-AML%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22STAR%20-%20Counts%22]%7D%7D]%7D&format=JSON': Timeout of 60 seconds was reached

I tried to update TCGAbiolinks via Github repos and update curl also, but it doesn't help.

Maybe someone experienced that problem too?

[Ram]

You might be interested in this other post: How to download Gene expression data and associate clinical data from TCGA

[shashankt693]

Hey, were you able to solve this issue. I am still getting the same error, I went through the issues on github and updated the package as well however the error still persists. I am hoping you found a solution

[Kevin Blighe]

To some, it would be better to retrieve the data manually via the Xena Browser:

• https://xenabrowser.net/datapages/
• https://xenabrowser.net/datapages/?cohort=GDC%20TARGET-AML&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443

Answer 1

[ATpoint]

Read the error, it says Timeout of 60 seconds was reached -- 60 seconds is the default timeput when downloading files in R. Do this: https://stackoverflow.com/questions/35282928/how-do-i-set-a-timeout-for-utilsdownload-file-in-r and set it to something like 3600. Big files take time, connection might be slow so increase timeout.

[shashankt693]

Thanks for pointing that out, naive mistake of not reading the error message completely.