Dave, Matt, Thanks for the comments. My Windows happens to be living in a Virtualbox on a Mac Pro, so that explains the overall sluggish pace! I guess that's part of the fun of needing the Agilent library.
Out of curiosity, I might try running one of the jobs on my own year- old laptop, just in case this is data related.. Cheers, bio.x2y On Feb 16, 9:26 pm, Matthew Chambers <[email protected]> wrote: > The delay in start up time for Agilent is a known issue. Unfortunately > the current Agilent API doesn't provide a way to get the list of scanIds > in a data file, nor a way to get a spectrum's scanId without getting its > data arrays. ProteoWizard is designed to support random access by > nativeID and by index to all of the data formats it supports, so it has > to enumerate all the spectra up front in order to get each of their > scanIds. On profile data, that takes a frustrating amount of time. > > I have a feature request pending with Agilent to get a function which > provides either a list of scanIds or a spectrum without metadata. > > Thanks for doing the comparison. I agree with Dave that the conversion > time sounds pretty long in both cases and I suspect a network share. > > -Matt > > > > bio.x2y wrote: > > Hi, > > > I independently used both Trapper (4.3.1) and Msconvert (pwiz 1.6.0) > > to convert a 1.4Gb Agilent MassHunter ".d" file containing ~16000 > > spectra to mzXML. > > > Parameters: > > $msconvert --mzXML --verbose large.d > > $trapper --mzXML -v large.d large.mzXML > > > Msconvert took 5hrs 38mins to complete, generating a 57Gb file. > > Trapper took 1hr 26mins to complete, generating a 28Gb file. > > > I can understand the differences in size, given the differences in > > structure and precision. However, the time difference still appears > > quite high. > > > One interesting observation is that msconvert does not start writing > > to the output file until 1hr 20min has elapsed. At that point, the > > file begins filling and the progress messages start appearing in the > > output. Trapper, on the other hand, starts filling the output file and > > reporting progress immediately. > > > I have seen this occur now for two runs on two different days, so I > > don't think it's related to other activity on the machine. > > > Perhaps msconvert is engaging in some preprocessing that isn't > > strictly necessary, for Agilent ".d" files at least? > > > Thanks, > > bio.x2y -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
