Hi David, As the post, I?m using TPP 5.1 in Windows 7. I think it's has an i5 with 12Gb of RAM.
It might not be that easy, as it is not only 1 data set that is broken. Are all data sets comprised of dimethylated samples with more than 10 fractions run on a QExactive. If I analyze single files (unfractionated), XPRESS runs without a problem. The same applies to data sets comprised with up to 7 fractions. I might have to think of a way to upload it because each data set would be around 20-30 Gb (13 fractions). Cheers, Alejandro On Wednesday, March 28, 2018 at 6:32:12 PM UTC+2, David Shteynberg wrote: > > 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] > <javascript:>> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
