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mksamur / RTCGAToolbox

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Failed getFirehoseData with dataset "GBMLGG" #45

Closed andreagrioni closed 1 year ago

andreagrioni commented 1 year ago

Hi, thanks for developing and maintaining the tool.

when running the cmd:

> RTCGAToolbox::getFirehoseData(
+     dataset="GBMLGG",
+     forceDownload=TRUE,
+     Mutation=TRUE # retrieve mutation data
+ )

output:

RTCGAToolbox cache directory set to:
    ~/.cache/R/RTCGAToolbox
trying URL 'https://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/GBMLGG/20160128/gdac.broadinstitute.org_GBMLGG.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 144423 bytes (141 KB)
==================================================
downloaded 141 KB

gdac.broadinstitute.org_GBMLGG.Clinical_Pick_Tier1.Level_4.2016012800.0.0
trying URL 'https://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/GBMLGG/20160128/gdac.broadinstitute.org_GBMLGG.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 6915094 bytes (6.6 MB)
==================================================
downloaded 6.6 MB

Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match
LiNk-NY commented 1 year ago

It looks like these datasets have different sets of columns. I've updated the code to merge both and include missing values. 9cde61906f535e9c01ea3a6d43c12ec5b73943c3 Best, Marcel