Hi Chris, Did you try: xinteract '*.pep.xml' -Ninteract.pep.xml -p0.05 -l9 -OAp -X-m0.15-nR,10-nK,8-L
(note the quotes around the input file 'glob'). --Luis On Thu, Apr 23, 2009 at 10:08 AM, Chris Hughes <[email protected]> wrote: > > I am having trouble getting this to work. I have 170 files in a > directory. > > If I navigate to the directory in command prompt and type: xinteract > *pep.xml it will go through all my files in terminal, but then at the > end there will be a --L"7"" exited with the non-zero exit code: 1 QUIT > - The job is incomplete > > Is there something I am doing wrong here? Ideally the command I would > like to run on all my files is: > > xinteract -Ninteract.pep.xml -p0.05 -l9 -OAp -X-m0.15-nR,10-nK,8-L > > Thanks! > > Chris > > > > On Apr 22, 3:18 pm, Luis Mendoza <[email protected]> wrote: > > Hello Kristian, > > Glad you were able to complete your analysis. One potential thing to > watch > > out for when you use wildcards (i.e. the asterisk) is that you may > > inadvertently include a file that you did not mean to, for example: an > old > > analysis file with the name interact-old.pep.xml ; this would naturally > > affect your results. > > > > As of now, there is no simple way to have Petunia get past the shell > limit > > on number of files/characters. Perhaps we could add an "Analyze all > pep.xml > > files in this directory" button or some such. Although in general I > would > > suggest using a command-line or even a script if you will be running > > analyses on very large numbers of files. > > Cheers, > > --Luis > > > > On Wed, Apr 22, 2009 at 12:00 PM, Kristian < > [email protected]>wrote: > > > > > > > > > Answered my own question. I was able to run the commands from Windows > > > command line. > > > > > the command >xinteract *.pep.xml analyzed all 120 of my .pep.xml > > > files. > > > > > I copied the command line from the petunia window to incorporate my > > > ICAT ratios and run protein prophet after: > > > >xinteract -Ndesiredfilename.pep.xml -p0.05 -l7 -Oip -X-m1.0-L > -A-lC-r0.5 > > > *.pep.xml > > > > > On Apr 22, 10:13 am, Kristian <[email protected]> wrote: > > > > I use petunia on a Windows machine, so there is no command line from > > > > my end. I use the default settings. I'm not even sure what Eric's > > > > post means. > > > > Is there a line I can edit in one of the GUI files to get around this > > > > limitation? Or otherwise, can I enter the commands in the Windows > > > > command line and get around it? > > > > > > On Apr 21, 4:26 pm, "Eric Deutsch" <[email protected]> > > > > wrote: > > > > > > > It is likely the shell that imposes the limit. > > > > > > > When you type: > > > > > > > xinteract *.pep.xml > > > > > > > the shell expands that wildcard into the full list before feeding > the > > > list > > > > > to xinteract. The shell has an inherent limit. xinteract does not. > For > > > this > > > > > very reason, you can get xinteract to the globbing for you with: > > > > > > > xinteract '*.pep.xml' > > > > > > > This causes the wildcard to be passed to xinteract and it will > resolve > > > it > > > > > for you. This has been used on over 35,000 pepXML files at once. It > > > works. > > > > > > > Eric > > > > > > > > -----Original Message----- > > > > > > From: [email protected] [mailto:spctools- > > > > > > [email protected]] On Behalf Of Brian Pratt > > > > > > Sent: Tuesday, April 21, 2009 4:11 PM > > > > > > To: [email protected] > > > > > > Subject: [spctools-discuss] Re: Limit on number of pep.xml files > that > > > can > > > > > > be analyzed with XInteract? > > > > > > > > There's not meant to be a limitation - can you give an example of > a > > > > > > command > > > > > > line that fails? > > > > > > > > -----Original Message----- > > > > > > From: [email protected] > > > > > > [mailto:[email protected]] On Behalf Of Kristian > > > > > > Sent: Tuesday, April 21, 2009 3:00 PM > > > > > > To: spctools-discuss > > > > > > Subject: [spctools-discuss] Re: Limit on number of pep.xml files > that > > > can > > > > > > be > > > > > > analyzed with XInteract? > > > > > > > > I have installed 4.2.1, but the problem persists. After a bit of > > > > > > experimenting, I've found that XInteract can only handle up to 99 > > > > > > input *.pep.xml files at a time. > > > > > > > > The operation fails with the message "failed: Operation not > > > > > > permitted". > > > > > > > > On Apr 16, 1:21 pm, Natalie Tasman <[email protected]> > > > wrote: > > > > > > > Hi Kristian, > > > > > > > > > Also, 4.2.1 contained many bug fixes. I'm not sure if this > would > > > have > > > > > > been > > > > > > > addressed, but it's always most efficient for us if you can try > to > > > > > > replicate > > > > > > > the issue on the latest version. > > > > > > > > > -Natalie > > > > > > > > > On Thu, Apr 16, 2009 at 12:42 PM, Christine Vogel > > > > > > <[email protected]>wrote: > > > > > > > > > > I have had some problems before if any of the pep.xml files > had > > > > > > identical > > > > > > > > names. Renaming them (and paths/names within the files) > solved > > > that > > > > > > > > problem. > > > > > > > > > > Christine > > > > > > > > > > On Thu, Apr 16, 2009 at 2:17 PM, Brian Pratt > > > > > > <[email protected]>wrote: > > > > > > > > > >> There's not meant to be a limitation - can you give an > example > > > of a > > > > > > > >> command > > > > > > > >> line that fails? > > > > > > > > > >> -----Original Message----- > > > > > > > >> From: [email protected] > > > > > > > >> [mailto:[email protected]] On Behalf Of > > > Kristian > > > > > > > >> Sent: Thursday, April 16, 2009 11:56 AM > > > > > > > >> To: spctools-discuss > > > > > > > >> Subject: [spctools-discuss] Limit on number of pep.xml files > > > that can > > > > > > be > > > > > > > >> analyzed with XInteract? > > > > > > > > > >> I'm using TPP 4.2.0 to analyze cleavable ICAT data from an > LCQ. > > > When > > > > > > > >> all replicates are done, I have 120 seperate .pep.xml files > to > > > > > > combine > > > > > > > >> and analyze. With earlier versions of TPP (i.e. 3.4) I > could > > > analyze > > > > > > > >> them all at once with Xinteract, but with 4.2 the operation > > > simply > > > > > > > >> aborts and fails with no error message. I can analyze the > files > > > 40 > > > > > > at > > > > > > > >> a time and then combine the interact.pep files in protein > > > prophet, > > > > > > but > > > > > > > >> I'm curious if and why there's a limitation on the number of > > > input > > > > > > > >> files for Xinteract.- Hide quoted text - > > > > > > > > > - Show quoted text -- Hide quoted text - > > > > > > > - Show quoted text -- Hide quoted text - > > > > > > - Show quoted text - > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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