A quick update. After running the same files with TPP 4.8, running time with ASAP ratio is quite reduced, to ~1h, but quantitation seems to work better with XPRESS.
Alejandro On Wednesday, November 19, 2014 7:29:30 PM UTC+1, Alejandro wrote: > > Hi all, > > I'm analyzing dimethylated data obtained with a QExactive using XTandem! > (have tried both static or variable searches). If the data is quantified > using Xpress, the time it takes is quite normal, ie fast, minute(s) or so > for a 1GB RAW file (ca. 250MB mzXML), however when activating ASAPratio, > the processing takes hundred times more than with Xpress (which reports a > quite disperse distribution of ratios, not seen with Orbitrap data, thus > the reason to see how ASAP performs). After looking in the list I found a > post which discussed somehow this > https://groups.google.com/d/topic/spctools-discuss/TkkoHpXAh4A/discussion > which was related to multithreading. > > When running this analysis the bottleneck seems to come from the ASAPratio: > > Stucked at: > > running: "C:/Inetpub/tpp-bin/XPressPeptideParser "interactasap.pep.xml" -m20 > -a -nn,8.04437027 -nK,8.04437027 -H -c5" > .................................................. 1k > .................................................. 2k > .................................................. 3k > .................................................. 4k > .................................................. 5k > .................................................. 6k > .................................................. 7k > . > command completed in 22 sec > > running: "C:/Inetpub/tpp-bin/ASAPRatioPeptideParser "interactasap.pep.xml" > -lnK -C -r0.02" > > > The same scenario as the one described in the old post seems to happen > here, only one core and ~50MB usage of RAM, using only > ASAPRatioPeptideParser.exe and this taking several hours to complete. > > Could it be also the mentioned "...redundant disk reads and base64 > decoding due to poor caching of the scans read from mzXML..." the cause? Or > it is just the nature of the data obtained with the Qexactive that makes it > take longer? I haven't checked if something would change by using an old > version of ASAPRatio ~2009 from that post. Though I don't think this would > be compatible with the current parsers. > > Any clues? > > 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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
