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I couldn't download data from the TCGA database. How do I need to fix it？ #460

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geng-lee opened this issue Mar 21, 2023 · 2 comments
Open

I couldn't download data from the TCGA database. How do I need to fix it？ #460

geng-lee opened this issue Mar 21, 2023 · 2 comments

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@geng-lee
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I couldn't download data from the TCGA database. How do I need to fix it？

Download and load most recent junction quantification and clinical data from

TCGA/FireBrowse for Breast Cancer

data <- loadFirebrowseData(folder=folder,

  •                        cohort="BRCA",

  •                        data=c("clinical", "junction_quantification",

  •                               "RSEM_genes"),

  •                        date="2016-01-28")

Loading...
| | 0%
Downloading files...
试开URL’http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz'
试开URL’http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz.md5'
试开URL’http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_Clinical.Level_1.2016012800.0.0.tar.gz'
试开URL’http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_Clinical.Level_1.2016012800.0.0.tar.gz.md5'
试开URL’http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.Level_3.2016012800.0.0.tar.gz'
试开URL’http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.Level_3.2016012800.0.0.tar.gz.md5'
试开URL’http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0.tar.gz'
试开URL’http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0.tar.gz.md5'
试开URL’http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0.tar.gz'
试开URL’http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0.tar.gz.md5'
Error in download.file(missingFiles, destfile = file.path(folder, basename(missingFiles))) :
cannot download any files
此外: Warning messages:
1: In download.file(missingFiles, destfile = file.path(folder, basename(missingFiles))) :
URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz': status was 'Failure when receiving data from the peer'
2: In download.file(missingFiles, destfile = file.path(folder, basename(missingFiles))) :
URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz.md5': status was 'Failure when receiving data from the peer'
3: In download.file(missingFiles, destfile = file.path(folder, basename(missingFiles))) :
URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_Clinical.Level_1.2016012800.0.0.tar.gz': status was 'Failure when receiving data from the peer'
4: In download.file(missingFiles, destfile = file.path(folder, basename(missingFiles))) :
URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_Clinical.Level_1.2016012800.0.0.tar.gz.md5': status was 'Failure when receiving data from the peer'
5: In download.file(missingFiles, destfile = file.path(folder, basename(missingFiles))) :
URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.Level_3.2016012800.0.0.tar.gz': status was 'Failure when receiving data from the peer'
6: In download.file(missingFiles, destfile = file.path(folder, basename(missingFiles))) :
URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__junction_quantification__data.Level_3.2016012800.0.0.tar.gz.md5': status was 'Failure when receiving data from the peer'
7: In download.file(missingFiles, destfile = file.path(folder, basename(missingFiles))) :
URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0.tar.gz': status was 'Failure when receiving data from the peer'
8: In download.file(missingFiles, destfile = file.path(folder, basename(missingFiles))) :
URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0.tar.gz.md5': status was 'Failure when receiving data from the peer'
9: In download.file(missingFiles, destfile = file.path(folder, basename(missingFiles))) :
URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0.tar.gz': status was 'Failure when receiving data from the peer'
10: In download.file(missingFiles, destfile = file.path(folder, basename(missingFiles))) :
URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/BRCA/20160128/gdac.broadinstitute.org_BRCA.Merge_rnaseq__illuminahiseq_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0.tar.gz.md5': status was 'Failure when receiving data from the peer'
@nuno-agostinho
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Hi @geng-lee, that is odd. Could you please try downloading again?

@nuno-agostinho
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Hi @geng-lee, did you have any luck with this issue?

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@nuno-agostinho @geng-lee