Yeah, that sounds bad, you can kill that because it's almost certainly still profile data. Did you use the exact syntax I gave for the filter parameter? --filter "peakPicking true [1,2]"
Just "peakPicking true [1,2]" is not enough. -Matt Zhi Sun wrote: > Hi Matt, > > I know it hasn't passed 2 hour :), but 30mins has passed, and it is still > loading the spectra. I just took a guess that the problem is stills there. > > Zhi > > -----Original Message----- > From: spctools-discuss@googlegroups.com > [mailto:spctools-disc...@googlegroups.com] On Behalf Of Matthew Chambers > Sent: Monday, October 05, 2009 9:56 AM > To: spctools-discuss@googlegroups.com > Subject: [spctools-discuss] Re: msconvert generated mzML file > > > It's impossible you had the same error you reported before: > > >> I ran into a problem. X!tandem took really long time (2 or more hours) >> > for loading the spectra, > > Since it hasn't been two hours, I know it must be a new error. Or at > least, it must have gotten to the error much faster. :) > > Presumably the file is now much smaller? > > -Matt > > > Zhi Sun wrote: > >> Thanks Brian. I just tried using the "peakPicking true [1,2]" to >> convert the file. It seems to produce the same error. >> >> Best, >> >> Zhi >> >> ------------------------------------------------------------------------ >> >> *From:* spctools-discuss@googlegroups.com >> [mailto:spctools-disc...@googlegroups.com] *On Behalf Of *Brian Pratt >> *Sent:* Monday, October 05, 2009 9:41 AM >> *To:* spctools-discuss@googlegroups.com >> *Subject:* [spctools-discuss] Re: msconvert generated mzML file >> >> Well, I learned something today! Sounds worth avoiding, though - >> msconvert is the coverter of choice moving forward. especially for >> mzML output. >> >> I'll have a quick look at the mzML and mzXML equivalent msconvert >> outputs from the X!Tandem point of view, since I'm the one that added >> that to X!Tandem. >> >> Brian >> >> On Mon, Oct 5, 2009 at 9:30 AM, Zhi Sun <z...@systemsbiology.org >> <mailto:z...@systemsbiology.org>> wrote: >> >> Hi Brian, >> >> I have post the mzML, mzXML and also the wiff file to >> http://www.peptideatlas.org/repository/tmp/ if anyone is interested in >> taking a look. >> >> ReAdw have an option -mzML, it is "EXPERIMENTAL". The version I used >> was 4.3.0. I haven't checked if there is a newer version out there. I >> have checked with my colleague with the X!tandem version. He said the >> X!tandem version we use should be same as the one in currently >> released TPP. >> >> Thanks, >> >> Zhi >> >> ------------------------------------------------------------------------ >> >> *From:* spctools-discuss@googlegroups.com >> <mailto:spctools-discuss@googlegroups.com> >> [mailto:spctools-discuss@googlegroups.com >> <mailto:spctools-discuss@googlegroups.com>] *On Behalf Of *Brian Pratt >> *Sent:* Monday, October 05, 2009 9:20 AM >> >> >> *To:* spctools-discuss@googlegroups.com >> <mailto:spctools-discuss@googlegroups.com> >> >> *Subject:* [spctools-discuss] Re: msconvert generated mzML file >> >> I don't think Readw ever made mzML files did it? Probably the user is >> thinking of mzXML there. >> >> X!Tandem's mzML reader is from the same library as msconvert's writer >> (assuming we're talking about the TPP build of X!Tandem), so a >> mismatch is unlikely. >> >> I think the problem probably isn't within the tools themselves, in >> this particular case, but in what data they're being fed. >> >> Brian >> >> On Fri, Oct 2, 2009 at 4:53 PM, Jimmy Eng <jke...@gmail.com >> <mailto:jke...@gmail.com>> wrote: >> >> >> I'll be a translator. Zhi seems to be having issues with ABI QQQ wiff >> files. They were translated to mzML using msconvert and X!Tandem >> didn't like them. She mentioned ReAdW only to state that X!Tandem was >> able to process some unrelated mzML files in the past. >> >> The problem could be: >> 1) the QQQ file really has no good ms/ms spectra in it. >> 2) there's a problem with the QQQ to mzML conversion. >> 3) everything's fine with the data but for whatever reason X!Tandem >> can't handle the particular mzML correctly. >> 4) the X!Tandem spectral processing parameters are set weird. >> >> Even money on the first 3. >> >> >> On Fri, Oct 2, 2009 at 4:31 PM, Matthew Chambers >> <matthew.chamb...@vanderbilt.edu >> <mailto:matthew.chamb...@vanderbilt.edu>> wrote: >> >>> I'm lost. You said "recently I used the msconvert to convert some QQQ >>> wiff files to mzML format". Are we talking about ABI WIFF or Thermo RAW? >>> >>> -Matt >>> >>> >>> Brian Pratt wrote: >>> >>>> You probably mean mzXML rather than mzML? >>>> >>>> On Fri, Oct 2, 2009 at 3:55 PM, Zhi Sun <z...@systemsbiology.org >>>> >> <mailto:z...@systemsbiology.org> >> >>>> <mailto:z...@systemsbiology.org <mailto:z...@systemsbiology.org>>> >>>> >> wrote: >> >>>> I just mean the mzML format itself. I used ReAdw to convert RAW >>>> file to mzML >>>> format. >>>> >>>> Thanks, >>>> Zhi >>>> >>>> >>>> -----Original Message----- >>>> From: spctools-discuss@googlegroups.com >>>> >> <mailto:spctools-discuss@googlegroups.com> >> >>>> <mailto:spctools-discuss@googlegroups.com >>>> >> <mailto:spctools-discuss@googlegroups.com>> >> >>>> [mailto:spctools-discuss@googlegroups.com >>>> >> <mailto:spctools-discuss@googlegroups.com> >> >>>> <mailto:spctools-discuss@googlegroups.com >>>> >> <mailto:spctools-discuss@googlegroups.com>>] On Behalf Of Matthew >> >>>> Chambers >>>> Sent: Friday, October 02, 2009 3:49 PM >>>> To: spctools-discuss@googlegroups.com >>>> >> <mailto:spctools-discuss@googlegroups.com> >> >>>> <mailto:spctools-discuss@googlegroups.com >>>> >> <mailto:spctools-discuss@googlegroups.com>> >> >>>> Subject: [spctools-discuss] Re: msconvert generated mzML file >>>> >>>> >>>> Hi Zhi, >>>> >>>> You say it worked fine with ReAdW; do you mean mzWiff? If so, what >>>> conversion settings did you use (for both msconvert and mzwiff)? >>>> >>>> -Matt >>>> >>>> >>>> Zhi Sun wrote: >>>> >>>>> Hi All, >>>>> >>>>> Recently I used the msconvert to convert some QQQ wiff files to mzML >>>>> >>>> format, >>>> >>>>> and did X!tandem search using those mzML files. I ran into a >>>>> >>>> problem. >>>> >>>>> X!tandem took really long time (2 or more hours) for loading the >>>>> >>>> spectra, >>>> >>>>> and them after it finally finished loading, it just reported >>>>> >>>> "Loaded, No >>>> >>>>> input spectra met the acceptance criteria." The X!tandem runs >>>>> >>>> fine on >>>> other >>>> >>>>> mzML file. I tested on one mzML which was generated by ReAdw before. >>>>> >>>>> When doing the conversion, I used default options for msconvert. >>>>> >>>> Does >>>> anyone >>>> >>>>> of you know what could be the reason for this? If necessary, I >>>>> >>>> could send >>>> >>>>> the wiff file and also the mzML file. >>>>> >>>>> Thanks, >>>>> Zhi >>>>> >> > > > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
