Ndtyjky

I am trying to replicate the process published here: https://dockflow.org/workflow/tcga//

The published code has been working perfectly up to the section saying: The clinical data can be obtained using TCGAbiolinks through two methods. The first method of downloading the indexed GDC clinical data works as expected:

lgg_clin <- GDCquery_clinic(project = "TCGA-LGG", type = "Clinical")

lgg_clin <- GDCquery_clinic(project = "TCGA-LGG", type = "Clinical")

clinical <- plyr::rbind.fill(gbm_clin,lgg_clin)

head(clinical)

The above shows realistic output (truncated below to conserve space):

head(clinical)
submitter_id classification_of_tumor last_known_disease_status updated_datetime primary_diagnosis tumor_stage age_at_diagnosis
1 TCGA-02-0001 not reported not reported 2018-09-06T13:49:07.196637-05:00 Glioblastoma not reported 16179
2 TCGA-02-0003 not reported not reported 2018-09-06T13:49:07.196637-05:00 Glioblastoma not reported 18341
3 TCGA-02-0004 not reported not reported 2018-09-06T13:49:07.196637-05:00 Glioblastoma not reported 21617

When the following code is run to get the clinical data the second way, i.e. from the clinical XML files:

query <- GDCquery(project = "TCGA-GBM"

                 ,data.category = "Clinical"

                 ,barcode = c("TCGA-08-0516"

                             ,"TCGA-02-0317"

                             )

                 )

GDCdownload(query)

clinical <- GDCprepare_clinic(query, clinical.info = "patient")

head(clinical)

...the following output (in yellow) and error is returned (in the gray section):

GDCdownload(query)
Downloading data for project TCGA-GBM
trying URL 'https://gdc.cancer.gov/system/files/authenticated%20user/0/gdc-> > client_v1.3.0_Windows_x64.zip'
Content type 'application/zip' length 16576709 bytes (15.8 MB)
downloaded 15.8 MB
GDCdownload will download: 2.579335 MB
Executing GDC client with the following command:
C:MyDirgdc-client.exe download -m gdc_manifest.txt
100% [#############################################] Time: 0:00:00 1.33 B/s
100% [#############################################] Time: 0:00:00 315.34 kB/s
100% [#############################################] Time: 0:00:00 109.00 kB/s
100% [#############################################] Time: 0:00:00 3.56 kB/s
100% [#############################################] Time: 0:00:00 258.15 kB/s
100% [#############################################] Time: 0:00:03 869.38 B/s
100% [#############################################] Time: 0:00:00 319.63 kB/s
100% [#############################################] Time: 0:00:00 830.89 kB/s
Successfully downloaded: 9

Error in move(i, file.path(path, i)) :

I could not find the file: c9cdbc76-105d-429b-9fce-f000819716f9

clinical <- GDCprepare_clinic(query, clinical.info = "patient")

Error in GDCprepare_clinic(query, clinical.info = "patient") : 

I couldn't find all the files from the query.Please check directory parameter right

It seems like there is data in "clinical" and based on the "Successfully downloaded: 9" message it appears there should be data somewhere so I am wondering how to get the GDCprepare_clinic() to get past the error to continue.

Thanks in advance.