Hello Alejandro, I am sorry that your pipeline crashes. Which version of the TPP are you using? Is it possible to have access to the broken dataset so I can trace the program's execution and pinpoint your issue? If you are able to, please post your mzML and pepXML file in the cloud for me to download and troubleshoot.
Cheers, -David On Wed, Mar 28, 2018 at 6:57 AM, Alejandro <[email protected]> wrote: > Hello all, > > I have been testing XPRESS again lately, I specially look forward to the > intensity based ratios. As in the title, XPRESS is failing with big > iProphet analyzed files. The files in question are experiments consisting > of 13 fractions of dimethylated (Formaldehyde "heavy" and "light", ie mass > change +28, +34) samples. > > The samples were analyzed with a QExactive, RAW files converted with > msconvert and then searched with MSGF+, as two static searches with mass > change at the n-termini and K (+28 or +34). Afterwards all validated and > combined with PeptideProphet followed by iProphet and ProteinProphet. All > models look fine, error rate seem to be fine. Comparison to other search > engines gives pretty similar results and quantification with other methods > (OpenMS FeatureFinderMultiplex) works fine, and can detect controls that we > have in. > > Now if I include XPRESS in the iProphet step, in experiments that have > ~6-7 fractions (~150 Mb pep.xml) XPRESS runs through without a problem, the > resulting ratios are centered around 0, and for the proteins I know they > are changed (Knockout/knockdown) I can see they are heavily reduced. > However, in experiments with ~13 fractions (~300 Mb pep.xml file) after the > petunia output reaches "...50-60k" (2-3 hours) it crashes without any > prompt (at the command line occurs the same); nonetheless ProteinProphet > continues and assembles proteins but of course no XPRESS is reported. I > have checked the RAM usage and is around 1-2Gb. XPRESS process on the > system monitor uses 25% (I have 4 cores, so using 1 processor), after some > hours the XPRESS process seems not be using any processor and RAM > consumption seems stable and then crashes. > > The command I have been using is as follows > > C:/TPP/bin/XPressPeptideParser interact_myname.ipro.pep.xml -m10 -a -b -i > -nn,6.031817 -nK,6.031817 -L -c5 > > I have also deactivated the reporting of intensity values, but it also > crashes. > > I don`t know if it is reaching a limit in the parsing of the xml file. For > other purposes I have parsed this big pep.xml files, the iProphet > validated, and I have had some troubles unless I call directly the nodes. > > Any thoughts? > > Thanks, > > Alejandro > > -- > 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/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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
