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hallamlab / MetaPathways

A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information
http://hallam.microbiology.ubc.ca/MetaPathways
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Step 15: Create PGDB not working #31

Closed xapple closed 11 years ago

xapple commented 11 years ago

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 commented 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

xapple commented 11 years ago

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)