Great to hear this, and please let me know if you find other problems. -David
On Wed, Mar 28, 2018 at 2:04 AM, Thibault Robin <[email protected]> wrote: > Dear David, > > It works properly now! I will have to do further testing on the rest of > the files to confirm it, but the problem seems to be fixed. > > Thank you for your time, > > Thibault > > 2018-03-27 18:29 GMT+02:00 David Shteynberg <David.Shteynberg@ > systemsbiology.org>: > >> 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 <[email protected]> >> 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 < >>> [email protected]>: >>> >>>> 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 <[email protected]> >>>> 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 < >>>>> [email protected]>: >>>>> >>>>>> 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 <[email protected]> >>>>>> 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 < >>>>>>> [email protected]>: >>>>>>> >>>>>>>> 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 <[email protected]> >>>>>>>> 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 < >>>>>>>>> [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 < >>>>>>>>>>> [email protected]>: >>>>>>>>>>> >>>>>>>>>>>> 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/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 < >>>>>>>>>>>>>>> [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 spctools-discuss+unsubscribe@g >>>>>>>>>>>>>>>> ooglegroups.com. >>>>>>>>>>>>>>>> To post to this group, send email to >>>>>>>>>>>>>>>> [email protected]. >>>>>>>>>>>>>>>> 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 >>>>>>>>>>>>>>> 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