Question

problem with getSRAfile in SRAdb

0

Entering edit mode

shidaxia • 0

@shidaxia-6966

Last seen 5.8 years ago

Hi,

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.

Thanks!

Tao

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

trying URL 'ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000648/SRR000648.sra'
downloaded 72 KB

trying URL 'ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000657/SRR000657.sra'
downloaded 276 KB

run study sample experiment
1 SRR000648 SRP000098 SRS000290 SRX000122
2 SRR000657 SRP000098 SRS000290 SRX000122
ftp
1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000648/SRR000648.sra
2 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000657/SRR000657.sra
> 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

locale:
[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

SRAdb • 2.2k views

ADD COMMENT • link updated 7.1 years ago by Jack Zhu ▴ 170 • written 7.1 years ago by shidaxia • 0

0

Entering edit mode

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 REPLY • link 7.1 years ago Sean Davis 21k

score 1 · Answer 1 · 2017-10-31

1

Entering edit mode

Jack Zhu ▴ 170

@jack-zhu-3338

Last seen 7.1 years ago

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:
'C:/Users/zhujack/Documents/R_WD'

trying URL 'ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000648/SRR000648.sra'
downloaded 280 KB

trying URL 'ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000657/SRR000657.sra'
downloaded 422 KB

run study sample experiment
1 SRR000648 SRP000098 SRS000290 SRX000122
2 SRR000657 SRP000098 SRS000290 SRX000122
ftp
1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000648/SRR000648.sra
2 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000657/SRR000657.sra

Jack

ADD COMMENT • link 7.1 years ago Jack Zhu ▴ 170

0

Entering edit mode

Hi Jack and Sean,

Just re-visit this problem. With newer R and SRAdb package, everything is fine now. Have no idea what happened. :-(

Tao

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

trying URL 'ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR000/SRR000648/SRR000648.sra'
downloaded 280 KB

trying URL 'ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR000/SRR000657/SRR000657.sra'
downloaded 422 KB

        run     study    sample experiment                                                                                                 ftp
1 SRR000648 SRP000098 SRS000290  SRX000122 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR000/SRR000648/SRR000648.sra
2 SRR000657 SRP000098 SRS000290  SRX000122 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR000/SRR000657/SRR000657.sra
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[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_1.42.2         RCurl_1.95-4.11      bitops_1.0-6         graph_1.58.0         BiocGenerics_0.26.0  RSQLite_2.1.1        RevoUtils_11.0.0    
[8] RevoUtilsMath_11.0.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18     compiler_3.5.0   pillar_1.3.0     bindr_0.1.1      tools_3.5.0      digest_0.6.16    bit_1.1-14       memoise_1.1.0   
 [9] tibble_1.4.2     pkgconfig_2.0.2  rlang_0.2.2      DBI_1.0.0        GEOquery_2.48.0  rstudioapi_0.7   bindrcpp_0.2.2   dplyr_0.7.6     
[17] xml2_1.2.0       hms_0.4.2        stats4_3.5.0     bit64_0.9-7      tidyselect_0.2.4 glue_1.3.0       Biobase_2.40.0   R6_2.2.2        
[25] limma_3.36.3     purrr_0.2.5      readr_1.1.1      tidyr_0.8.1      blob_1.1.1       magrittr_1.5     assertthat_0.2.0 crayon_1.3.4

ADD REPLY • link 5.8 years ago shidaxia • 0