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 <[email protected]> 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 [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.
