Dear David, The pepXML file generation is now working properly for all files after fixing the file names. However, I unfortunately still have issues with PTMProphet for some of the files. Sometimes even within the same datasets some files work and others don't.The thing is that I checked the differences between a working and a non working one but everything seems to be correct. All the paths are correct, the spectrum indexes are correct and properly described in the corresponding mzML file. All I get is a "segmentation fault (core dumped)" error.
Do you have any idea what is going on ? Thank you, Thibault 2018-02-12 18:18 GMT+01:00 David Shteynberg < [email protected]>: > 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 <[email protected]> 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_bRP0 >> 1_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@systemsbiolo >> gy.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 < >>> [email protected]> 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 <[email protected]> >>>> 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 < >>>>> [email protected]>: >>>>> >>>>>> 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 <[email protected]> >>>>>> 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 [email protected]. >>>>>>> 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 >>>>>> [email protected]. >>>>>> 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 [email protected]. >>>>> To post to this group, send email to [email protected] >>>>> . >>>>> 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 >>> [email protected]. >>> To post to this group, send email to [email protected]. >>> 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 [email protected]. >> To post to this group, send email to [email protected]. >> 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/ > topic/spctools-discuss/6srdMeRzmd8/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To post to this group, send email to [email protected]. > 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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