Question

Errors in TCGAbiolinks

0

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sabarinath.chandrasekharan ▴ 10

@sabarinathchandrasekharan-11149

Last seen 7.5 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

tcgabiolinks • 2.0k views

ADD COMMENT • link updated 7.7 years ago by Tiago Chedraoui Silva ▴ 260 • written 7.7 years ago by sabarinath.chandrasekharan ▴ 10

score 0 · Answer 1 · 2016-08-05

0

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Tiago Chedraoui Silva ▴ 260

@tiago-chedraoui-silva-8877

Last seen 3.7 years ago

Brazil - University of São Paulo/ Los A…

Hi, I'm sorry. We are still improving/developping the code and the version that was build in bioconductor had a bug, it should be solved very soon as we have already pushed the fix For the moment, please use the github version. You can installing with the following command devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")

ADD COMMENT • link 7.7 years ago Tiago Chedraoui Silva ▴ 260

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Thank you very much for your support!

ADD REPLY • link 7.7 years ago sabarinath.chandrasekharan ▴ 10

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Hi, I tried the github version, but that also is throwing an error

> query <- GDCquery(project = "TARGET-AML",
+                   data.category = "Transcriptome Profiling",
+                   data.type = "Gene Expression Quantification", 
+                   workflow.type = "HTSeq - Counts"
+ )
Error in open.connection(con, "rb") : 
  Server returned nothing (no headers, no data)

ADD REPLY • link 7.7 years ago sabarinath.chandrasekharan ▴ 10

1

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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?

> query <- GDCquery(project = "TCGA-ACC", data.category = "Copy Number Variation",
+                   data.type = "Copy Number Segment",
+                   barcode = c( "TCGA-OR-A5KU-01A-11D-A29H-01", "TCGA-OR-A5JK-01A-11D-A29H-01"))
Parsed with column specification:
cols(
  released = col_character(),
  state = col_character(),
  dbgap_accession_number = col_character(),
  primary_site = col_character(),
  disease_type = col_character(),
  project_id = col_character(),
  name = col_character()
)
https://gdc-api.nci.nih.gov/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=360&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:[%22TCGA-ACC%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Copy%20Number%20Variation%22]%7D%7D]%7D
> GDCdownload(query)
GDCdownload will download: 73.387 KB compressed in a tar.gz file
Downloading as: Thu_Aug_11_20_31_01_2016.tar.gz
Downloading: 15 kB      
Error in if (!(md5sum(file) == manifest$md5[i])) { : 
  missing value where TRUE/FALSE needed
>

Please advice!

ADD REPLY • link 7.7 years ago sabarinath.chandrasekharan ▴ 10

0

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having same issue.

Tx

ADD REPLY • link 7.7 years ago tbc2113 • 0

0

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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.

ADD REPLY • link 7.7 years ago Tiago C. Silva ▴ 270