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 unsubscribe from this topic, visit >>>>>>>>>> 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