Step 15: Create PGDB not working

[xapple]

The pipeline seems to complete only up to the final step where the pathological software is called. Here is the error message:

WARNING: Refseq annotation is not scheduled!
         Taxonomic information will not be found in the annotation table.

  **********************************************************
  **************** Running  MetaPathways *******************
  **********************************************************
              /bubo/home/h3/lucass/HUMIC/processed_test/samples/f-erken/clean/clean.fasta
  **********************************************************



Issuing Command : /bubo/home/h3/lucass/proj38/nobackup/metapathways/libs/python_scripts/MetaPathways_filter_input.py  --min_length 0 --log_file /bubo/home/h3/lucass/HUMIC/processed_test/samples/f-erken/metapathways/output//clean/run_statistics//clean.nuc.stats  -i /bubo/home/h3/lucass/HUMIC/processed_test/samples/f-erken/clean/clean.fasta -o  /bubo/home/h3/lucass/HUMIC/processed_test/samples/f-erken/metapathways/output//clean/preprocessed//clean.fasta -M /bubo/home/h3/lucass/HUMIC/processed_test/samples/f-erken/metapathways/output//clean/preprocessed//clean.mapping.txt

1. Running Quality Check ......... Success!

[...... snip ......]

14. Making MLTreeMap Images  ......... Skipping!


Issuing Command : /bubo/home/h3/lucass/proj38/nobackup/pathwaytools/aic-export/pathway-tools/ptools/17.0/pathway-tools -patho /bubo/home/h3/lucass/HUMIC/processed_test/samples/f-erken/metapathways/output//clean/ptools// -no-taxonomic-pruning  -no-web-cel-overview

15. Create PGDB  ......... Error!
Error! : ;; Optimization settings: safety 1, space 0, speed 3, debug 1.
;; For a complete description of all compiler switches given the
;; current optimization settings evaluate (EXPLAIN-COMPILER-SETTINGS).

*** This Pathway Tools executable built on Thu Mar 28, 2013 at 22:05:01. ***
[Scanning PGDB directories   /gulo/proj_nobackup/b2011138/pathwaytools/ptools-local/pgdbs/user/
                             /gulo/proj_nobackup/b2011138/pathwaytools/ptools-local/pgdbs/registry/
                             /gulo/proj_nobackup/b2011138/pathwaytools/aic-export/pgdbs/biocyc/   4 PGDBs found]
[Opened acache database /gulo/proj_nobackup/b2011138/pathwaytools/aic-export/pathway-tools/ocelot-acache/, which contains 1 ocelot KBs]
[Reading Pathway Tools init file "/gulo/proj_nobackup/b2011138/pathwaytools/ptools-local/ptools-init.dat" ]
[Start downloading patches...
If any patches are being installed, they are listed in the terminal window.
Looking for patches in
  http://bioinformatics.ai.sri.com/ptools/17.0/Linux-64/patches/
No patches need to be installed.
... done downloading patches]
[Redirecting standard-output and error-output to /bubo/home/h3/lucass/HUMIC/processed_test/samples/f-erken/metapathways/output/clean/ptools/pathologic.log]

batch-pathologic: A fatal error occurred for /bubo/home/h3/lucass/HUMIC/processed_test/samples/f-erken/metapathways/output/clean/ptools/ version 1.0.
See pathologic log file /bubo/home/h3/lucass/HUMIC/processed_test/samples/f-erken/metapathways/output/clean/ptools/pathologic.log for more details.

And here is the content of the pathologic.log file:

16-Jul-2013  22:55:55
Started processing /bubo/home/h3/lucass/HUMIC/processed_test/samples/f-erken/metapathways/output/clean/ptools/
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 ...)

Any idea how to solve the problem ?

[nielshanson]

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

[xapple]

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)