This looks like a problem with the RT model in PeptideProphet. SSRCalc3.pl seems to be failing on some peptide in your file. Perhaps there is a problem with the retention times or scan numbers in your input pep.xml files. It appears you are processing Mascot results, but you did not change the names of the .dat files. What exact steps did you undertake to generate the pep.xml files? To get past this immediate issue you can disable the RT model in PeptideProphet and you should be able to see results.
-David On Thu, Jul 15, 2010 at 5:42 AM, KMackay <[email protected]> wrote: > It is giving the following error in the log files... > > PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909091257 > (MinGW)) akel...@isb > read in 0 1+, 5907 2+, 4978 3+, 933 4+, 132 5+, 21 6+, and 6 7+ > spectra. > Initialising statistical models ... > Iterations: .........10.........20....Estimating Retention Time > Model ... please wait ... > Assertion failed: probs->size() == run_RT_count_, file Parsers/ > Algorithm2XML/RTCalculator.cxx, line 279 > > This application has requested the Runtime to terminate it in an > unusual way. > Please contact the application's support team for more information. > > command "C:/Inetpub/tpp-bin/PeptideProphetParser > "F006140.interact.pep.xml" MINPROB=0.05 PI RT" failed: Unknown error > > command "C:/Inetpub/tpp-bin/PeptideProphetParser > "F006140.interact.pep.xml" MINPROB=0.05 PI RT" exited with non-zero > exit code: 255 > QUIT - the job is incomplete > > command "c:\Inetpub\tpp-bin\xinteract -NF006140.interact.pep.xml - > p0.05 -l7 -OIRp c:/Inetpub/wwwroot/ISB/data/140/F006140.pep.xml" > failed: Unknown error > > Command FAILED > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
