Hi Thibault, Please rename your tandem result file to 20131226_HeLa_bRP01_120min.xml, then run Tandem2XML and this problem should disappear.
Cheers, -David On Mon, Feb 12, 2018 at 2:42 AM, Thibault Robin <vyns...@gmail.com> wrote: > Dear David, > > I tried your options but it looks like my version of X!Tandem does not > support the zlib compression. > However the mzML conversion seems to work fine otherwise, the tail end of > the mzML looking as supposed. But this time it produces warning even at the > Tandem2XML step: > > > > > > > *Incomplete file name. No file loaded: Incomplete file name. No file > loaded: Incomplete file name. No file loaded: Incomplete file name. No file > loaded: WARNING: Failed to open mzML file. Output will not contain > retention times.* > > The path in the tandem result file is however correct so I don't really > understand why it cannot read it.. > > Link mzML: > https://www.dropbox.com/s/4m2btbnfsnmkaty/20131226_HeLa_ > bRP01_120min.mzML?dl=0 > > Link Tandem result: > https://www.dropbox.com/s/9t87tu3a9uq6i50/output_1_ > 20131226_HeLa_bRP01_120min.2018_02_09_01_26_09.t.xml?dl=0 > > What is really frustrating is that the dataset where I only have the mgf > does work perfectly fine after converting it to mzML, despite having a > badly formatted tail end... > > Thibault > > > 2018-02-06 2:37 GMT+01:00 David Shteynberg <David.Shteynberg@ > systemsbiology.org>: > >> I will also add that the file I generated by converting from raw here, >> with options from my earlier message, didn't exclude any scans but did >> apply peak picking and 32 bit encoding. My file is 327 megabytes but your >> files are about 1.3 gigabytes. >> So if you are concerned about space I would recommend converting with >> the my options. >> >> >> >> On Mon, Feb 5, 2018 at 5:32 PM, David Shteynberg < >> david.shteynb...@systemsbiology.org> wrote: >> >>> Thibault, >>> >>> I checked both files and it appears they both reference the scans >>> correctly. I am not sure why the two files would be of different >>> size/content if you ran the gui and commandline with the same set of >>> options. This would be a question for the proteowizard/msconvert >>> developers. From the TPP standpoint both should work ok. >>> >>> -David >>> >>> On Mon, Feb 5, 2018 at 1:00 PM, Thibault Robin <vyns...@gmail.com> >>> wrote: >>> >>>> Maybe I confused the files, sorry if that is the case. >>>> >>>> However there is indeed a difference between the conversion through >>>> command lines or the GUI: >>>> Results of a file comparison: >>>> ***** gui.mzML >>>> ccession="MS:1000040" unitName="m/z"/> >>>> <cvParam cvRef="MS" accession="MS:1000796" name="spectrum >>>> title" value="a.1.1. File:"a.raw", NativeID:" >>>> ;controllerType=0 controllerNumber=1 scan=1""/> >>>> <scanList count="1"> >>>> ***** cmd.mzML >>>> ccession="MS:1000040" unitName="m/z"/> >>>> <scanList count="1"> >>>> ***** >>>> [...] >>>> >>>> Here is the mzML converted using the GUI: >>>> https://www.dropbox.com/s/7lne9itvgexhcm8/gui.mzML?dl=0 >>>> >>>> And the one with command lines: >>>> https://www.dropbox.com/s/l2bbyz3rzo22pmi/cmd.mzML?dl=0 >>>> >>>> Both converted just now from the raw file. >>>> >>>> I will have to try tomorrow to see how this impact the tandem results >>>> >>>> Thibault >>>> >>>> >>>> 2018-02-05 21:05 GMT+01:00 David Shteynberg < >>>> david.shteynb...@systemsbiology.org>: >>>> >>>>> You can try sending me your mzML file again, but the one I have states >>>>> that the input was an mgf file: >>>>> >>>>> <fileDescription> >>>>> <fileContent> >>>>> <cvParam cvRef="MS" accession="MS:1000580" name="MSn spectrum" >>>>> value=""/> >>>>> <cvParam cvRef="MS" accession="MS:1000127" name="centroid >>>>> spectrum" value=""/> >>>>> </fileContent> >>>>> <sourceFileList count="1"> >>>>> <sourceFile id="_x0032_0131226_HeLa_bRP01_120min.mgf" >>>>> name="20131226_HeLa_bRP01_120min.mgf" location="file:////media/vynsk >>>>> ir/Seagate/HeLa/MGF/PXD00 >>>>> 1441"> >>>>> <cvParam cvRef="MS" accession="MS:1000774" name="multiple >>>>> peak list nativeID format" value=""/> >>>>> <cvParam cvRef="MS" accession="MS:1001062" name="Mascot MGF >>>>> format" value=""/> >>>>> </sourceFile> >>>>> </sourceFileList> >>>>> </fileDescription> >>>>> >>>>> >>>>> On Mon, Feb 5, 2018 at 10:07 AM, Thibault Robin <vyns...@gmail.com> >>>>> wrote: >>>>> >>>>>> Hi David, >>>>>> >>>>>> I really think the mzML was converted from a raw file. But I think I >>>>>> understand the problem. I am using msconvert through the GUI since I am >>>>>> not >>>>>> a fan of Dos, and I just realized that one of the default parameters is >>>>>> >>>>>> >>>>>> *"titleMaker <RunId>.<ScanNumber>.<ScanNumber>.<ChargeState> >>>>>> File:"<SourcePath>", NativeID:"<Id>"* >>>>>> Could it be the root of the problem ? However when I remove it it >>>>>> automatically reappears in the parameter file... >>>>>> Am I forced to use command lines ? >>>>>> >>>>>> Cheers, >>>>>> >>>>>> Thibault >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "spctools-discuss" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to spctools-discuss+unsubscr...@googlegroups.com. >>>>>> To post to this group, send email to spctools-discuss@googlegroups. >>>>>> com. >>>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to a topic in the >>>>> Google Groups "spctools-discuss" group. >>>>> To unsubscribe from this topic, visit https://groups.google.com/d/to >>>>> pic/spctools-discuss/6srdMeRzmd8/unsubscribe. >>>>> To unsubscribe from this group and all its topics, send an email to >>>>> spctools-discuss+unsubscr...@googlegroups.com. >>>>> To post to this group, send email to spctools-discuss@googlegroups.com >>>>> . >>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to spctools-discuss+unsubscr...@googlegroups.com. >>>> To post to this group, send email to spctools-discuss@googlegroups.com. >>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "spctools-discuss" group. >> To unsubscribe from this topic, visit https://groups.google.com/d/to >> pic/spctools-discuss/6srdMeRzmd8/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> spctools-discuss+unsubscr...@googlegroups.com. >> To post to this group, send email to spctools-discuss@googlegroups.com. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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