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HYPHY Package >> HyPhy bugs >> undefined environment varible when trying to use GARD
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Message started by florent on Mar 9th, 2012 at 4:33am

Title: undefined environment varible when trying to use GARD
Post by florent on Mar 9th, 2012 at 4:33am
Hi,

I got some erors while trying to run GARD from batch files. the errors are still of the same type : the program seems to not interpret environment variables such as PROMPT_FOR_FILE or DATAFILE_TREE and returns error saying these are wrong values.

for instance, when tryng to run the orginal GARD.bf script, I get this output:

Initialized GARD on 20 MPI nodes.
Population size is 38 models

/usr/remote/hyphy/HYPHY/TemplateBatchFiles/Nucleotide file to screen::
/usr/remote/hyphy/HYPHY/TemplateBatchFiles/Nucleotide file to screen::
Master node received an error:
Could not find source dataset file:PROMPT_FOR_FILE Path stack: {/var/spool/torqu
e/tmpdir/1420633.pbil-torque.univ-lyon1.fr/,/usr/remote/hyphy/HYPHY/TemplateBatchFiles/}
Call stack
1 : Read Data Set ds from file PROMPT_FOR_FILE

whereas the name of file given to the prompt is actually present in the first directory of the Path stack.

another call with a custom version of GARD where I try to provide the tree topology. Again, the program bumps on an environment variable:

Initialized GARD on 20 MPI nodes.
Population size is 38 models

/var/spool/torque/tmpdir/1389590.pbil-torque.univ-lyon1.fr/Nucleotide file to sc
reen::
Master node received an error:
Illegal right hand side in call to Tree id = ...; it must be a string, a Newick
tree spec or a topology
Call stack
1 : Build Tree givenTree from string DATAFILE_TREE


Maybe it come from missing libraries or parameter definitions... Can you lpease help me about this?

Thanks in advance.

Florent

Title: Re: undefined environment varible when trying to use GARD
Post by Sergei on Mar 16th, 2012 at 11:10pm
Hi Florent,

The error messages are a bit misleading -- PROMPT_FOR_FILE simply causes HyPhy to read the path to the file from stdin, at which point the program complains that it can't find the file specified in that path.

It seems that torque (your queue manager) launches the job (and HyPhy) in a temporary directory (e.g. /var/spool/torqu
e/tmpdir/1420633.pbil-torque.univ-lyon1.fr/), but the data file are not placed there. When you specify pathnames to alignment files and tree files, try using absolute pathnames (e.g. /home/user/data/test.fas) and not relative ones (e.g. data/test.fas), and see if that helps.

Sergei

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