Closed xapple closed 11 years ago
Hey there,
16-Jul-2013 22:55:55 Fatal error: An organism with ID CLEAN already exists.
Evaluation stack:
->(TPL::ZOOM-COMMAND :FROM-READ-EVAL-PRINT-LOOP NIL ...)
(SYS::..RUNTIME-OPERATION "applyn" :UNKNOWN-ARGS)
(TPL:DO-COMMAND "zoom" :FROM-READ-EVAL-PRINT-LOOP ...)
It seems that a PGDB folder already exists in your ptools-local/pgdbs/user directory. This is where Pathway Tools stores all the user created PGDBs.
Pathway tools seems to have a problem with creating multiple PGDBs with the same name. Trying clearing out this folder and running the pipeline again. Let me know how that goes.
Niels
Hey,
Thanks for the reply. That was indeed it. These two added lines in the pipeline and it's fine.
self.pgdb_path = pathwaytools_dir + 'ptools-local/pgdbs/user/' + self.sample.name + 'cyc'
if os.path.exists(self.pgdb_path): shutil.rmtree(self.pgdb_path)
The pipeline seems to complete only up to the final step where the pathological software is called. Here is the error message:
And here is the content of the
pathologic.log
file:Any idea how to solve the problem ?