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?
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.
Thanks for pointing that out, naive mistake of not reading the error message completely.
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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
To some, it would be better to retrieve the data manually via the Xena Browser: