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 < [email protected]>: > 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 >>>>>>>>>>>>>> topic in the Google 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