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sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
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Bad istream when reading mzML file #249

Closed ricoderks closed 2 years ago

ricoderks commented 2 years ago

Hi Steffen,

I've been using XCMS for quite a while now and love it! I'am now trying to read some SIM data with the function readSRMData from MSnbase package, but I'am getting the following error:

Error: Can not open file /home/ricoderks/Documents/LUMC/Projects/prot_eisa/Data/mzML/sir/080621_sir_std_conv_100nM_1.mzML! Original error was: Error in pwizModule$open(filename): [SpectrumList_mzML::create()] Bad istream.
11.
stop("Can not open file ", filename, "! Original error was: ", e, call. = FALSE)
10.
value[[3L]](cond)
9.
tryCatchOne(expr, names, parentenv, handlers[[1L]])
8.
tryCatchList(expr, classes, parentenv, handlers)
7.
tryCatch(pwizModule$open(filename), error = function(e) { stop("Can not open file ", filename, "! Original error was: ", e, call. = FALSE) })
6.
mzR::openMSfile(x, backend = NULL)
5.
.openMSfile(x)
4.
FUN(X[[i]], ...)
3.
lapply(files, function(x) { msf <- .openMSfile(x) if (!is(msf, "mzRpwiz")) stop("Can only extract chromatogram information from a mzML file", ...
2.
lapply(files, function(x) { msf <- .openMSfile(x) if (!is(msf, "mzRpwiz")) stop("Can only extract chromatogram information from a mzML file", ...
1.
MSnbase::readSRMData(files = mzml_files[49])

I traced it back to openMSfile. I compared it to previous files I tried to read and the only difference I can find is the amount of SIM traces.

I'am using mzR 2.26.1, MSnbase 2.18.0 and xcms 3.14.1.

Can you help me with this? If needed I can send / upload you the mzML file.

Cheers, Rico

 version  R version 4.1.1 (2021-08-10)
 os       Ubuntu 20.04.2 LTS          
 system   x86_64, linux-gnu           
 ui       RStudio                     
 language en_GB                       
 collate  en_GB.UTF-8                 
 ctype    en_GB.UTF-8                 
 tz       Europe/Amsterdam            
 date     2021-08-16   

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ricoderks commented 2 years ago

A small update. I recreated the mzML files with msconvert (using the docker container from proteowizard) with the parameter --noindex and now it is possbile to read the files. I don't know why it goes wrong if you don't use this parameter. It looks like the issue is not with mzR.