Hello Thibault, I have verified that the 5.1.0 version of Tandem2XML has this problem on your datafile (and likely on all Tandem version Vengeance files). I have also verified that the newer development code of Tandem2XML (that will be made available in a future release but for now is only available from our source code repository) resolves this issue . I have placed a windows development executable that solves the issue at the following link: https://www.dropbox.com/s/bx8rutwv6za0hx6/Tandem2XML.exe?dl=0 Can you verify that it corrects the problem on your system?
Thank you, -David On Fri, Mar 23, 2018 at 2:01 AM, Thibault Robin <vyns...@gmail.com> wrote: > Here is the tandem result file: > https://www.dropbox.com/s/w5ba10g13abzxp4/1_Ctrl_2.xml?dl=0 > > To generate the pepXML file I use Tandem2XML followed by InteractParser as > you recommended previously. > > Thanks, > > Thibault > > 2018-03-22 18:28 GMT+01:00 David Shteynberg <David.Shteynberg@ > systemsbiology.org>: > >> Hello Thibault, >> >> It still appears that your pep.xml file has incorrect spectrum names. >> Which a problem upstream of the PTMProphet analysis. The failing >> spectrum_query is >> >> <spectrum_query spectrum="controllerType=0 controllerNumber=1 >> scan=8431.08430.08430.2" start_scan="8430" end_scan="8430" >> precursor_neutral_mass="1805.8098" assumed_charge="2" index="1981" >> retention_time_sec="4435.913"> >> >> The scan number is off by one and PTMProphet is trying to extract scan >> 8430 (which has 0 peaks) instead of the correct scan 8431 (which has 392 >> peaks). The off by one error means NONE of the PSMs correspond to the mzML >> spectrum that PTMProphet is extracting for localization and NONE of >> localizations will be valid. >> >> Do you have the tandem xml output for this search and a description of >> the steps taken to get to the pepXML file you posted? >> >> Thanks, >> -David >> >> On Thu, Mar 22, 2018 at 8:08 AM, Thibault Robin <vyns...@gmail.com> >> wrote: >> >>> Here is a file that fails: >>> https://www.dropbox.com/s/xycfgnxwxxdlstc/1_Ctrl_2.int.xml?dl=0 >>> with the mzML if needed: >>> https://www.dropbox.com/s/gdyahhobb3o0q3q/1_Ctrl_2.mzML?dl=0 >>> >>> It seems to work for a while but it ends up crashing: >>> >>> >>> >>> >>> *INFO: Reading file 1_Ctrl_2.int.xml ...INFO: processed 500/2003 >>> spectrum_queries.INFO: processed 1000/2003 spectrum_queries.INFO: processed >>> 1500/2003 spectrum_queries.Segmentation fault (core dumped)* >>> >>> As if one of the spectrum is causing troubles. >>> >>> Thank you for your time, >>> >>> Thibault >>> >>> >>> >>> >>> >>> >>> 2018-03-22 15:26 GMT+01:00 David Shteynberg < >>> david.shteynb...@systemsbiology.org>: >>> >>>> Hi Thibault, >>>> >>>> I cannot tell you what the issue is without having access to your >>>> dataset files. Can you post the files that break your analysis for me to >>>> pull down and test? >>>> >>>> Thanks, >>>> -David >>>> >>>> On Thu, Mar 22, 2018 at 5:19 AM, Thibault Robin <vyns...@gmail.com> >>>> wrote: >>>> >>>>> 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 < >>>>> david.shteynb...@systemsbiology.org>: >>>>> >>>>>> 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_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.shteynb...@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/vynskir/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+unsubscribe@g >>>>>>>>>>>> ooglegroups.com. >>>>>>>>>>>> To post to this group, send email to >>>>>>>>>>>> spctools-discuss@googlegroups.com. >>>>>>>>>>>> Visit this group at https://groups.google.com/grou >>>>>>>>>>>> p/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 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