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.shteynb...@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 <vyns...@gmail.com> 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 < >> david.shteynb...@systemsbiology.org>: >> >>> 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 <vyns...@gmail.com> >>> 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 < >>>> david.shteynb...@systemsbiology.org>: >>>> >>>>> 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 < >>>>> david.shteynb...@systemsbiology.org> 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 <vyns...@gmail.com> >>>>>> 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 < >>>>>>> david.shteynb...@systemsbiology.org>: >>>>>>> >>>>>>>> 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 <vyns...@gmail.com> >>>>>>>> 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+unsubscr...@googlegroups.com. >>>>>>>>> To post to this group, send email to >>>>>>>>> spctools-discuss@googlegroups.com. >>>>>>>>> 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 >>>>>>>> d8/unsubscribe. >>>>>>>> To unsubscribe from this group and all its topics, send an email to >>>>>>>> spctools-discuss+unsubscr...@googlegroups.com. >>>>>>>> To post to this group, send email to spctools-discuss@googlegroups. >>>>>>>> com. >>>>>>>> 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 the Google >>>>>>> Groups "spctools-discuss" group. >>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>> send an email to spctools-discuss+unsubscr...@googlegroups.com. >>>>>>> To post to this group, send email to spctools-discuss@googlegroups. >>>>>>> com. >>>>>>> Visit this group at https://groups.google.com/group/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/to >>>>> pic/spctools-discuss/6srdMeRzmd8/unsubscribe. >>>>> To unsubscribe from this group and all its topics, send an email to >>>>> spctools-discuss+unsubscr...@googlegroups.com. >>>>> To post to this group, send email to spctools-discuss@googlegroups.com >>>>> . >>>>> Visit this group at https://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -- >>>> 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+unsubscr...@googlegroups.com. >>>> To post to this group, send email to spctools-discuss@googlegroups.com. >>>> Visit this group at https://groups.google.com/group/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/to >>> pic/spctools-discuss/6srdMeRzmd8/unsubscribe. >>> To unsubscribe from this group and all its topics, send an email to >>> spctools-discuss+unsubscr...@googlegroups.com. >>> To post to this group, send email to spctools-discuss@googlegroups.com. >>> Visit this group at https://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- >> 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+unsubscr...@googlegroups.com. >> To post to this group, send email to spctools-discuss@googlegroups.com. >> Visit this group at https://groups.google.com/group/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/6srdMeRzmd8/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- 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+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
