Hi Jimmy- The directory does have the .out files (as that is what I thought I needed to use for the pepXML conversion). Please correct me if I'm wrong... I just looked through several of the data directories that I have tried and received this error for, and I don't have any files with the repeating zeros like that, but the do look like this:
(i selected several) RG_81_2.11179.11179.2 RG_81_2.14447.14447.2 RG_81_2.271.271.2 Thank! Ruby On Mar 1, 4:08 pm, Jimmy Eng <jke...@gmail.com> wrote: > Ruby, > > The problem likely has nothing to do with the -Etrypsin option in the > Out2XML command. Do you have a bunch of *.out files in the directory > c:\Inetpub\wwwroot\ISB\data\RG_81_2\ > > Are those files named something like RG_81_2.00001.00001.1.out? > > - Jimmy > > On Tue, Mar 1, 2011 at 1:58 PM, Ruby <rgund...@jhmi.edu> wrote: > > Hi- > > I just downloaded the latest version of TPP this week, so version: > > TPP v4.4 VUVUZELA rev 1, Build 201010121551 (MinGW) > > > I'm still really hoping for an answer for the -Etrypsin error.....I'm > > stuck until I get that figured out. > > > Thanks!! > > Ruby > > > On Feb 28, 12:04 pm, Joe Slagel <jsla...@systemsbiology.org> wrote: > >> Hi Rudy, > > >> For both questions you have, what version of TPP are you using? and I'm > >> assuming you are trying to convert the .RAW to mzXML using the petunia > >> interface? (And I'll defer to others on your first question...unless you > >> don't get an answer). > > >> -Joe > > >> On Sat, Feb 26, 2011 at 6:02 PM, Ruby <rubycell7...@gmail.com> wrote: > >> > Hi- > >> > 1) I'm trying to use the TPP to process my Sequest search results. > >> > (since I have access to sequest only on a cluster, I'm not able to use > >> > the TPP to setup the search, which is what I'd like to do). Rather, > >> > I'm trying to use the .out files for peptide & proteinprophet > >> > processing. > > >> > However, I get this error when I try to process my directory that has > >> > the .out files from the Sequest search. > > >> > command "c:\Inetpub\tpp-bin\Out2XML c:/Inetpub/wwwroot/ISB/data/ > >> > RG_81_2 1 -Etrypsin" failed: Unknown error > > >> > Is this due to the fact that I did a semi-enzyme search? How can I > >> > work around this? I didn't see a semi-enzyme choice in the 'options' > >> > section of the convert to pepXML page. > > >> > 2) I'd like to do an XTandem search via the TPP. When I try to > >> > convert .RAW to mzXML, I get this error: > >> > 'c:\Inetpub\tpp-bin\ReAdW' is not recognized as an internal or > >> > external command, operable program or batch file. > > >> > I thought that TPP wasn't using ReAdW anymore, but rather the > >> > MSConverter. I have downloaded the MSFileReader, but what parts of > >> > that go in the tpp-bin directory?? Basically, how do I get it > >> > configured so that it uses MSConvert for processing the .RAW files? > > >> > Thanks! > >> > Ruby > > >> > -- > >> > You received this message because you are subscribed to the Google Groups > >> > "spctools-discuss" group. > >> > To post to this group, send email to spctools-discuss@googlegroups.com. > >> > To unsubscribe from this group, send email to > >> > spctools-discuss+unsubscr...@googlegroups.com. > >> > For more options, visit this group at > >> >http://groups.google.com/group/spctools-discuss?hl=en. > > >> -- > >> Joe Slagel > >> Institute for Systems Biology > >> jsla...@systemsbiology.org > >> (206) 732-1362 > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to spctools-discuss@googlegroups.com. > > To unsubscribe from this group, send email to > > spctools-discuss+unsubscr...@googlegroups.com. > > For more options, visit this group > > athttp://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 spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
