Thibault, I have placed a version of this tool compiled under linux at the following link:
https://www.dropbox.com/s/vb0lh3wwo4acgop/Tandem2XML?dl=0 Hopefully this one will run on your system. -David On Sun, Mar 25, 2018 at 11:42 PM, Thibault Robin <vyns...@gmail.com> wrote: > Dear David, > > Thank you very much for finding a fix for the issue ! Is it however > possible to get the linux version ? My whole workflow is already set up so > it would be much easier for me. > > Cheers, > > Thibault > > 2018-03-23 20:19 GMT+01:00 David Shteynberg <David.Shteynberg@ > systemsbiology.org>: > >> 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.shteynb...@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 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