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Question: SRAdb package - problems
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gravatar for Jack Zhu
4.4 years ago by
Jack Zhu170
Jack Zhu170 wrote:
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/SRR000 648.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/SRR000 657.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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