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jshelton
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@jshelton-11836
Last seen 8.0 years ago
Hi,
I am attempting to download data but instead get a file with the extension '.tar.gz'. However, this is not a compressed file. It is a text file with the words:
{
"message": "internal server error"
}
Below is the code I ran:
samples <- c("TCGA-BA-4074", "TCGA-BA-4075")
interesting.genes <- c("TP53", "PIK3CA", "FAT1")
query.exp <- GDCquery(project = "TCGA-HNSC",
legacy = TRUE,
data.category = "Gene expression",
data.type = "Gene expression quantification",
platform = "Illumina HiSeq",
file.type = "results",
experimental.strategy = "RNA-Seq",
barcode = samples)
GDCdownload(query.exp)
Thanks for your help
Hi,
I was able to run the code here.Please, what is your session info? And what query.exp$results shows?
Best regards,
Tiago
My output shows this
> GDCdownload(query.exp)GDCdownload will download 2 files. A total of 3.031802 MB
Downloading as: Fri_Nov_11_09_35_27_2016.tar.gz
Downloading: 1.2 MB [1] 1
> GDCprepare(query.exp)|=======================================================================================================================================================| 100%
Downloading genome information. Using: Homo sapiens genes (GRCh37.p13)
Starting to add information to samples
=> Add clinical information to samples
=> Adding subtype information to samples
Subtype information from:doi:10.1038/nature14129
class: RangedSummarizedExperiment
dim: 20330 2
metadata(0):
assays(2): raw_count scaled_estimate
rownames(20330): A1BG|1 A1CF|29974 ... ZZEF1|23140 ZZZ3|26009
rowData names(4): gene_id entrezgene ensembl_gene_id transcript_id.transcript_id_TCGA-BA-4075-01A-01R-1436-07
colnames(2): TCGA-BA-4075-01A-01R-1436-07 TCGA-BA-4074-01A-01R-1436-07
colData names(62): sample patient ... subtype_Copy.Number subtype_PARADIGM
> data <- GDCprepare(query.exp)
|==================================================================| 100%
Downloading genome information. Using: Homo sapiens genes (GRCh37.p13)
Starting to add information to samples
=> Add clinical information to samples
=> Adding subtype information to samples
Subtype information from:doi:10.1038/nature14129
> query.exp$results
[[1]]
center.code center.name center.short_name center.center_id center.namespace center.center_type data_type updated_datetime
1276 07 University of North Carolina UNC ee7a85b3-8177-5d60-a10c-51180eb9009c unc.edu CGCC Gene expression quantification 2016-09-07T11:17:30.997957-05:00
1425 07 University of North Carolina UNC ee7a85b3-8177-5d60-a10c-51180eb9009c unc.edu CGCC Gene expression quantification 2016-09-07T11:17:30.997957-05:00
file_name md5sum data_format acl access platform state state_comment file_id data_category file_size
1276 unc.edu.85034d8f-c10c-4db2-ade2-f26ea7cf2d95.1507611.rsem.genes.results 654b40396ed647c6ba22c3fbaf963b1b TXT open open Illumina HiSeq live NA 9bbe732f-4592-4681-91ee-d9e00c88ef1c Gene expression 1508723
1425 unc.edu.78a8e33e-fd10-4dcd-b8fd-aad93db18c45.1484374.rsem.genes.results 2faf952fe332870fbec90dbe81b96b2b TXT open open Illumina HiSeq live NA 20a606f9-2aef-489b-a1d6-0044533e96ff Gene expression 1523079
cases submitter_id type tags experimental_strategy tissue.definition
1276 TCGA-BA-4075-01A-01R-1436-07 NA file v2, unnormalized, gene RNA-Seq Primary solid Tumor
1425 TCGA-BA-4074-01A-01R-1436-07 NA file v2, unnormalized, gene RNA-Seq Primary solid Tumor