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 Groups "spctools-discuss" group. >>>>>>>>>>>> To 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