Question: OMA, GOdata/Wget error
gravatar for protistologist
4.0 years ago by
protistologist0 wrote:

I am having an issue trying oma with the "ToyExample" on my server.

I get the errors WARNING: GO data is not present (./.oma//GOdata.drw). Use GOdownload() to obtain it. Error, (in wget) wget failed

Any help would be greatly appreciated.

darwin godownload oma orthologs • 1.4k views
ADD COMMENTlink modified 4.0 years ago by adrian.altenhoff660 • written 4.0 years ago by protistologist0

This is a just hunch based on the error you have reported but it looks like either you don't have wget installed on your system or a firewall between you and where ever OMA is trying to go is preventing wget from connecting.

ADD REPLYlink written 4.0 years ago by genomax89k
gravatar for adrian.altenhoff
4.0 years ago by
adrian.altenhoff660 wrote:

The error you observed is caused by a ubuntu specific problem. we took the chance to release a bug-fix version (1.1.2). Thanks for reporting.

ADD COMMENTlink written 4.0 years ago by adrian.altenhoff660


In trying to work around a DB conversion issue with an array, I tried to use only the -c option, but got the following error: Error, (in ConvertRawFile) Darwin cannot open file /n/sw/fasrcsw/apps/Core/OMA/\ 1.1.2-fasrc01/bin/../bin/../darwinlib/../data/GOdata.drw-20161213 to write to: \ No such file or directory

I tried moving to this folder to find it but couldn't. Any idea on how to fix that? Using the latest 1.1.2


ADD REPLYlink written 3.8 years ago by tauanacunha0
gravatar for Christophe Dessimoz
4.0 years ago by
University College London
Christophe Dessimoz700 wrote:

Please make sure that you are using the latest version (currently 1.1.1), which also attempts to use curl if wget in unavailable.

Also, with this latest version, if you don't need function annotations, you can bypass the problem altogether. Just add the following line to your parameter file:

DoGroupFunctionPrediction := false;

ADD COMMENTlink written 4.0 years ago by Christophe Dessimoz700
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