Question: problem with getSRAfile in SRAdb
gravatar for shidaxia
3 months ago by
shidaxia0 wrote:


Try to run the code in SRAdb vignette.  It seems getSRAfile only downloads a portion of .sra files (the actual file size for these two files are 280 and 422kB.  I've tried other files and the problem is still there.




> getSRAfile( c("SRR000648","SRR000657"), sra_con, fileType = 'sra' )
Files are saved to: 

trying URL ''
downloaded 72 KB

trying URL ''
downloaded 276 KB

        run     study    sample experiment
1 SRR000648 SRP000098 SRS000290  SRX000122
2 SRR000657 SRP000098 SRS000290  SRX000122
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SRAdb_1.36.0         RCurl_1.95-4.8       bitops_1.0-6         graph_1.54.0         BiocGenerics_0.22.0  RSQLite_2.0         
[7] RevoUtilsMath_10.0.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11     XML_3.98-1.6     digest_0.6.12    R6_2.2.0         DBI_0.6-1        stats4_3.4.0     httr_1.2.1      
 [8] rlang_0.1.1      blob_1.1.0       RevoUtils_10.0.4 tools_3.4.0      bit64_0.9-7      Biobase_2.36.2   bit_1.1-12      
[15] yaml_2.1.14      compiler_3.4.0   pkgconfig_2.0.1  memoise_1.1.0    GEOquery_2.42.0  tibble_1.3.3  

ADD COMMENTlink modified 3 months ago by Jack Zhu170 • written 3 months ago by shidaxia0

SRAdb just downloads the file from the link in your post, so this isn't really a problem with SRAdb specifically, I suspect. Could you try doing the download outside of R? Also, could you check the file size on your disk as well as the value reported by R?

ADD REPLYlink written 3 months ago by Sean Davis21k
gravatar for Jack Zhu
3 months ago by
Jack Zhu170
Jack Zhu170 wrote:

Hi Tao,

I tested the same code on a Windows and a Mac and both downloaded the files with correct size.  Are you using a 64-bit Windows?  Have you tried what Sean suggested?

> getSRAfile( in_acc = c("SRR000648","SRR000657"), sra_con = sra_con, destDir = getwd(), fileType = 'sra' )
Files are saved to: 

trying URL ''
downloaded 280 KB

trying URL ''
downloaded 422 KB

        run     study    sample experiment
1 SRR000648 SRP000098 SRS000290  SRX000122
2 SRR000657 SRP000098 SRS000290  SRX000122


ADD COMMENTlink written 3 months ago by Jack Zhu170
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