search

hallamlab / metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
http://hallam.microbiology.ubc.ca/MetaPathways/
33 stars 14 forks source link

MetaPathways 2.5.2 Fails at Running PathoLogic Step #100

Open JSkar opened 5 years ago

JSkar commented 5 years ago

Hi!

MetaPathways seems to get stuck when trying to run the Pathologic step. Here is the error I get:

RUNNING PATHOLOGIC Fixing file /home/joe/ptools-local/pgdbs/user/desulfobulbus_propionicus_dsm2032cyc/1.0/input/organism.dat ERROR Failed to run Pathologic on input /home/joe/MetaPathways/TestOutput/Desulfobulbus_propionicus_DSM2032/ptools// : INFO Kill any other PathwayTools instance running on the machine and try again ERROR ERROR Failed to run Pathologic on input /home/joe/MetaPathways/TestOutput/Desulfobulbus_propionicus_DSM2032/ptools// : ERROR Exiting the Python code

Any ideas as to why this is happening? I have tried restarting the machine and installed PathwayTools and MetaPathways on a completely different machine and tried it that way, too with no luck. Both of the machines were running Ubuntu 18.04.1 64-bit.

I have attached my template_param and _config files along with the output from the command I ran.

template_config.txt template_param.txt Command Log

Thanks! Joe