Hi David, Adding /usr/local/tpp/bin to my path solved the problem. Thanks very much for the prompt reply. Alex
On Tuesday, October 2, 2018 at 9:40:29 AM UTC-7, David Shteynberg wrote: > > Hi Alex, > > What is the content of your PATH environment variable? You can check with > echo $PATH command. You should add the directory with TPP binaries ( > /usr/local/tpp/bin ) to you PATH. The way to do this depends on your > shell. > > In bash shell do this: > export PATH=/usr/local/tpp/bin:$PATH > > In C shell do this: > setenv PATH /usr/local/tpp/bin:$PATH > > Let me know if it still gives the same message after changing the PATH. > > -David > > > On Tue, Oct 2, 2018 at 9:24 AM Alex Zelter <aze...@uw.edu <javascript:>> > wrote: > >> Hi there, >> >> I am using TPP v5.2.0-b1 Flammagenitus Pre-release Beta, Build >> 201809101205-7809 (Linux-x86_64) with Kojak pep.xml data running the >> following command: >> >> /usr/local/tpp/bin/xinteract -Ninteract.pep.xml -p0 -l1 -eT -PPM -OAPdp >> -drandom_ -ip file1.pep.xml file3.pep.xml file3.pep.xml >> >> This command runs to completion, however looking in the output I see: >> >> .... >> running: "/usr/local/tpp/bin/ProphetModels.pl -i interact.pep.xml -d >> "random_"" >> Analyzing interact.pep.xml ... >> .... >> => Total so far: 134784 hits. (3317 decoys, 0 excluded) >> Using decoy ratio of 0.0284042151512031 for PeptideProphet. >> Inserting decoy analysis tags in line 4542 of interact.pep.xml >> Running tpp_models... >> *Can't exec "tpp_models.pl <http://tpp_models.pl>": No such file or >> directory at /usr/local/tpp/bin/ProphetModels.pl line 1179.* >> Done >> command completed in 35 sec >> ... >> >> Should I be concerned by this? I get this error twice during the run. >> Later in the output the same command is run but this time a filename is >> given to tpp_models.pl and the program then runs with no errors: >> >> >> running: "/usr/local/tpp/bin/tpp_models.pl '/path/to/interact.pep.xml'" >> File: /path/to/interact.pep.xml >> - in ms run: /path/to/file1... >> - in ms run: /path/to/file2... >> - in ms run: /path/to/file3... >> >> ------------------------------------------------------------------------------- >> TPP DASHBOARD -- started at Mon Oct 1 16:03:50 2018 >> >> ------------------------------------------------------------------------------- >> File /path/to/interact.pep.xml is pepxml >> Found fval (+1) model... >> etc... >> >> tpp_models.pl is present and executable on the computer's filesystem so >> I assume this error is due to tpp_models.pl not being given a file to >> operate on in the instances where there is a "no such file" error. >> >> Am I safe to ignore this? >> Thanks! >> Alex >> >> -- >> 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-discu...@googlegroups.com <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
