[BioC] SRAdb package - problems
Jack Zhu
zhujack at mail.nih.gov
Thu Jun 13 16:31:11 CEST 2013
Hi Preethy,
It looks like you are running a old version of SRAdb, which might be
problematic since both NCBI SRA and EBI ERA has had some changes and
the functions in SRAdb have been updated accordingly. The following
is my test with correct commands in newer version of SRAdb:
---------------------
> sra_dbname <- 'SRAmetadb.sqlite'
> sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname)
> getSRAfile( in_acc = c("SRR000648","SRR000657"), sra_con = sra_con, destDir = getwd(), fileType = 'sra', srcType='ftp' )
Files are saved to:
'/Users/zhujack/Documents/R'
trying URL 'ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000648/SRR000648.sra'
ftp data connection made, file length 287153 bytes
opened URL
==================================================
downloaded 280 Kb
trying URL 'ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000122/SRR000657/SRR000657.sra'
ftp data connection made, file length 432401 bytes
opened URL
==================================================
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
> getFASTQinfo( in_acc = c("SRR000648","SRR000657"), srcType = 'ftp' )
study sample experiment run analysis
organism instrument.platform instrument.model library.name
library.layout
1 SRP000098 SRS000290 SRX000122 SRR000648 null Tachyglossus
aculeatus LS454 454 GS FLX 2036546523
SINGLE
2 SRP000098 SRS000290 SRX000122 SRR000657 null Tachyglossus
aculeatus LS454 454 GS FLX 2036546523
SINGLE
library.strategy library.source library.selection run.read.count
run.base.count file.name file.size
md5
1 FL-cDNA TRANSCRIPTOMIC cDNA 378
99533 SRR000648.fastq.gz 82Kb
c5e254dac864ac78d48a03e21038b110
2 FL-cDNA TRANSCRIPTOMIC cDNA 598
158519 SRR000657.fastq.gz 133Kb
fec6ea0767b6fe661278dbd1cdfe9e43
ftp
1 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR000/SRR000648/SRR000648.fastq.gz
2 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR000/SRR000657/SRR000657.fastq.gz
> getSRAfile( in_acc = c("SRR000648","SRR000657"), sra_con = sra_con, destDir = getwd(), fileType = 'fastq', srcType='ftp' )
Files are saved to:
'/Users/zhujack/Documents/R'
trying URL 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR000/SRR000648/SRR000648.fastq.gz'
ftp data connection made, file length 84837 bytes
opened URL
==================================================
downloaded 82 Kb
trying URL 'ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR000/SRR000657/SRR000657.fastq.gz'
ftp data connection made, file length 136727 bytes
opened URL
==================================================
downloaded 133 Kb
study sample experiment run analysis
organism instrument.platform instrument.model library.name
library.layout
1 SRP000098 SRS000290 SRX000122 SRR000648 null Tachyglossus
aculeatus LS454 454 GS FLX 2036546523
SINGLE
2 SRP000098 SRS000290 SRX000122 SRR000657 null Tachyglossus
aculeatus LS454 454 GS FLX 2036546523
SINGLE
library.strategy library.source library.selection run.read.count
run.base.count file.name file.size
md5
1 FL-cDNA TRANSCRIPTOMIC cDNA 378
99533 SRR000648.fastq.gz 82Kb
c5e254dac864ac78d48a03e21038b110
2 FL-cDNA TRANSCRIPTOMIC cDNA 598
158519 SRR000657.fastq.gz 133Kb
fec6ea0767b6fe661278dbd1cdfe9e43
ftp
1 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR000/SRR000648/SRR000648.fastq.gz
2 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR000/SRR000657/SRR000657.fastq.gz
----------------------
> sessionInfo()
R version 3.0.0 Patched (2013-04-10 r62546)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
other attached packages:
SRAdb_1.14.0
-----------------------
So you might need to upgrade your R/Biconductior version to get newer
version of SRAdb. Please let me know if you still see any problems or
have any questions.
----
Yuelin Jack Zhu
Genetics Branch/CCR/NCI/NIH
Tel: (301)496-4527
FAX: (301) 402-3241
E-mail: zhujack at mail.nih.gov
On Thu, Jun 13, 2013 at 6:43 AM, Preethy Nair <preethy.nair at helsinki.fi> wrote:
> Dear Jack Zhu,
>
> I was trying to use SRAdb package to download the SRA files in fatsq format
> and am experiencing some problems. Could you advice me on this ?
>
>
> I was trying the code mentioned in the package manual and getting the
> following errors:
> ====================================================
> getSRAfile (in_acc=c("SRR000648","SRR000657"), sra_con=sra_con,
> destdir=getwd(), sraType='ftp')
> BUt I am getting the below error:
> cannot open URL
> 'ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/ftp/SRX/SRX000/SRX000122/SRR000648/SRR000648.sra'
>
> =======================================
> getSRAfile( c("SRR000648","SRR000657"), sra_con, fileType = 'sra' )
> Error in getSRAfile(c("SRR000648", "SRR000657"), sra_con, fileType = "sra")
> :
> unused argument(s) (fileType = "sra")
> getFASTQinfo( c("SRR000648","SRR000657"), srcType = 'ftp' )
> Error: could not find function "getFASTQinfo"
>
> =====================================
> getSRAfile( c("SRR000648","SRR000657"), sra_con, fileType = 'fastq' )
> Error in getSRAfile(c("SRR000648", "SRR000657"), sra_con, fileType =
> "fastq") :
> unused argument(s) (fileType = "fastq")
>
> ===================================================
>
> Hope you can help me with this. Especially with the "getFASTQinfo" method
> and with the "getSRAfile"
>
>
> Thanks a lot,
> Preethy
>
> --
> Preethy S Nair, DVM, MSc,
> Department of Medical Genetics,
> Faculty of Medicine,
> University of Helsinki.
>
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