MSnbase package, Error in downloading data file "PXD000001" from PRIDE Repository by pxget function
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fgol ▴ 10
@fgol-19486
Last seen 2.2 years ago

Hello,

I want to download this raw data file "PXD000001" from the PRIDE repository. However I faced with the below Error:

library("MSnbase")
library("rpx")
px1 <- PXDataset("PXD000001")
mzf <- pxget(px1, 6)


Downloading 1 file
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/README.txt'
Error in download.file(urls[i], toget[i], ...) : 
  cannot open URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/README.txt'
In addition: Warning message:
In download.file(urls[i], toget[i], ...) :
  InternetOpenUrl failed: 'The login request was denied

> ms <- openMSfile(mzf)
Error in openMSfile(mzf) : object 'mzf' not found

Can you please advice me how can I fix this problem and successfully download this data into my RStudio?

Thank you very much.

MSnbase Bioconductor PRIDE rpx PXDataset • 1.0k views
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Entering edit mode

Hello, I have the same exact problem.

I am doing a tutorial about Quantitative Proteomics using rpx to import data an PXDataset keep giving me error in fpt connexion. Is there any way to load all needed data into "px1" without the need to download it from fpt? I downloaded all needed files in local. I both tried from behind a firewall and not.

Thank you very much for your help

gianluigi

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Yes, indeed, if you have local files, you can provide their full path as input to the openMSfile() function. This is also what happens in the example above, except that the path to the local file is extracted from the rpx cache once it has been downloaded.

I would highly advise to have a look at the more recent Bioconductor packages and teaching material, all described in the R for Mass Spectrometry handbook.

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@laurent-gatto-5645
Last seen 9 days ago
Belgium

It looks like there was a problem to access and download files from the PRIDE ftp server. Things seem to work on my end now:

> library(rpx)
> px1 <- PXDataset("PXD000001")
> px1
Object of class "PXDataset"
 Id: PXD000001 with 12 files
 [1] 'F063721.dat' ... [12] 'generated'
 Use 'pxfiles(.)' to see all files.
> pxfiles(px1)
 [1] "F063721.dat"                                                         
 [2] "F063721.dat-mztab.txt"                                               
 [3] "PRIDE_Exp_Complete_Ac_22134.xml.gz"                                  
 [4] "PRIDE_Exp_mzData_Ac_22134.xml.gz"                                    
 [5] "PXD000001_mztab.txt"                                                 
 [6] "README.txt"                                                          
 [7] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML" 
 [8] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML"
 [9] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML"         
[10] "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw"           
[11] "erwinia_carotovora.fasta"                                            
[12] "generated"                                                           
> mzf <- pxget(px1, 6)
Downloading 1 file
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/README.txt'
Content type 'unknown' length 1645 bytes
==================================================
> mzf
[1] "/home/lg390/tmp/README.txt"

There is however another point you need to be careful with. File number 6 isn't a raw file, but the README file. You need to first check file indices to identify those that you want to downloaded. In this case, it seems to be file number 7.

> mzf <- pxget(px1, 7)
Downloading 1 file
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML'
Content type 'unknown' length 450032788 bytes (429.2 MB)
==================================================
> mzf
[1] "/home/lg390/tmp/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"
> openMSfile(mzf)
Mass Spectrometry file handle.
Filename:  TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML 
Number of scans:  7534
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Dear Laurent, Thank you very much. You are right, it shows file number 6 is README file. However, still I have the same problem when I try to open file number 7, and also 8.

> px1 <- PXDataset("PXD000001")
> mzf <- pxget(px1, 7)
Downloading 1 file
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML'
Error in download.file(urls[i], toget[i], ...) : 
  cannot open URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML'
In addition: Warning message:
In download.file(urls[i], toget[i], ...) :
  InternetOpenUrl failed: 'The login request was denied'


> mzf <- pxget(px1, 8)
Downloading 1 file
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML'
Error in download.file(urls[i], toget[i], ...) : 
  cannot open URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML'
In addition: Warning message:
In download.file(urls[i], toget[i], ...) :
  InternetOpenUrl failed: 'The login request was denied'
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Entering edit mode

This could be something on your side. Are you behind a firewall? Could you try to set setInternet2(TRUE) or see these other related issues: https://stackoverflow.com/questions/33355444/r-when-trying-to-install-package-internetopenurl-failed and https://stackoverflow.com/questions/25599943/unable-to-install-packages-in-latest-version-of-rstudio-and-r-version-3-1-1.

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