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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
