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sabarinath.chandrasekharan
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@sabarinathchandrasekharan-11149
Last seen 8.1 years ago
Hi,
I am having trouble with two modules of TCGAbiolinks (re-installed yesterday)
1. GDCdownload
and
2. GDCquery_Maf
GDCdownload gives the following error, whenever used
> query <- GDCquery(project = "TARGET-AML", + data.category = "Transcriptome Profiling", + data.type = "Gene Expression Quantification", + workflow.type = "HTSeq - Counts") https://gdc-api.nci.nih.gov/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=1163&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]%7D > GDCdownload(query) Downloading as: Fri_Aug_05_11_18_18_2016.tar.gz Error in gzfile(path.expand(tarfile), "rb") : cannot open the connection In addition: Warning messages: 1: running command 'curl -o Fri_Aug_05_11_18_18_2016.tar.gz --remote-header-name --request POST 'https://gdc-api.nci.nih.gov/legacy/data' --data @Payload' had status 127 2: In gzfile(path.expand(tarfile), "rb") : cannot open compressed file 'Fri_Aug_05_11_18_18_2016.tar.gz', probable reason 'No such file or directory' >
GDCquery_Maf gives an error like an infinite loop, and finally the R crashes.
Please advice.
Sabari
Thank you very much for your support!
Hi, I tried the github version, but that also is throwing an error
Hi, the GDCquery is now working as it should, but GDCdownload is downloading only a partial file.
Note: I am behind a university proxy, could it be due to this?
Please advice!
having same issue.
Tx
Hi,
They update GDC to version 2.0 and there was a change in the API. I fixed it, it should be very soon in the bioconductor. Version 2.0.3 and 2.1.3.
The GDCquery error happend because their server was down for maintenance.
Please, could you test with the github version for the moment.