Hi Adam, Thanks for submitting the bug report. I have traced it to a problem with iProphet processing small files. I have corrected the issue and have a patch here: https://www.dropbox.com/s/mq9yv5a4ew9umhe/InterProphetParser.exe?dl=0
Please replace your existing copy in C:\TPP\bin\InterProphetParser.exe with the one from my patch and try again. Cheers, -David On Mon, Oct 23, 2017 at 12:51 PM, Adam R <[email protected]> wrote: > Hi David, > > I have attached a screenshot of the parameters used, and have also > attached screenshots of the output of the command. I figure there are a few > abundant peptides that should make it through iProphet... > > Best, > > Adam > > > > On Monday, October 23, 2017 at 1:51:08 PM UTC-5, David Shteynberg wrote: >> >> I have run the TPP on MSFragger results, including iProphet, before. >> What parameters did you use for PeptideProphet? What was the output of >> that command? Is it possible that you don't have any high scoring PSM left >> after PeptideProphet filtering? >> >> Thanks, >> -David >> >> On Mon, Oct 23, 2017 at 11:42 AM, Adam R <[email protected]> wrote: >> >>> Hi Everyone, >>> >>> I am running into a problem with iProphet when trying to perform >>> additional validation on PeptideProphet files sourced from MSFragger >>> pep.xml output. The command fails and >>> shows the warning "file not found: not created or deleted?" Has anyone >>> else had this issue before? I would like to be able to use MSFragger output >>> files (wide mass search) and feed the resulting output through >>> PeptideProphet/iProphet/PTMProphet. >>> >>> Thanks, >>> >>> Adam >>> >>> >>> -- >>> 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. > -- 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.
