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 <David.Shteynberg@ > 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 <[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 [email protected]. >>>>>>>>>> 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 >>>>>>>>> https://groups.google.com/d/topic/spctools-discuss/6srdMeRzm 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