Step 15: EOF file error.

[sunitj]

All the steps work just fine until I reach step 15. And then I get the following errors:

STDERR:

15. Create PGDB  ......... Error!
Error! : ;; Optimization settings: safety 1, space 1, speed 3, debug 2.
;; For a complete description of all compiler switches given the
;; current optimization settings evaluate (EXPLAIN-COMPILER-SETTINGS).

*** This Pathway Tools executable built on Sat Oct 12, 2013 at 0:53:03. ***
[Scanning PGDB directories   /opt/packages/pathway-tools/data/ptools-local/pgdbs/user/
                             /opt/packages/pathway-tools/data/ptools-local/pgdbs/registry/
                             /opt/packages/pathway-tools/17.5/aic-export/pgdbs/biocyc/   3 PGDBs found]
[Opened acache database /opt/packages/pathway-tools/17.5/aic-export/pathway-tools/ocelot-acache/, which contains 1 ocelot KBs]
Warning: No Pathway Tools init file was found at:
         "/opt/packages/pathway-tools/data/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/17.5/Linux-64/patches/
No patches need to be installed.
... done downloading patches]
[Redirecting standard-output and error-output to Lau_207/Lau_207/ptools/pathologic.log]

batch-pathologic: A fatal error occurred for Lau_207/Lau_207/ptools/ version 1.0.
See pathologic log file Lau_207/Lau_207/ptools/pathologic.log for more details.

The 'pathologic.log' file:

13-Feb-2014  15:45:13 
Started processing Lau_207/Lau_207/ptools/
13-Feb-2014  15:45:13 Fatal error: eof encountered on stream #<EXCL:FILE-SIMPLE-STREAM #P"/opt/packages/pathway-tools/17.5/aic-export/PGDB-counter.dat" closed @ #x1002ef0c672>
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 ...)

When I check this file (PGDB-counter.dat), it's empty. Should it have something from the installation of the pathway-tools?

EDIT: I should have mentioned this earlier, Pathway-Tools is running fine on it's own.

System Information: OS: RHEL6 Processors: 32 RAM: 512GB Versions:

• Metapathways v 1.0
• pathway-tools v 17.5

[nielshanson]

Hey there,

I haven't run into this problem before... When I look at mine all it contains is this number

shebop:~ nielsh$ more pathway-tools-175/aic-export/PGDB-counter.dat 

102

I'm not sure what this corresponds to as I don't have 102 PGDBs loaded

Have you tried building the PGDB directly from the ptools/ folder produced by MetaPathways directly from the pathway-tools executable

e.g.

<pathway-tools>/pathway-tools -patho <mp_output>/<sample>/ptools/ -no-taxonomic-pruning -no-web-cel-overview

Also check the contents of the ptools/ directory there should be a few files in there

shebop:ptools nielsh$ ls -la *
-rw-r--r--  1 nielsh  staff  7638638 13 Jan 15:20 0.fasta
-rw-r--r--  1 nielsh  staff  1765304 13 Jan 15:20 0.pf
-rw-r--r--  1 nielsh  staff       65 13 Jan 15:20 genetic-elements.dat
-rw-r--r--  1 nielsh  staff      128 13 Jan 15:20 organism-params.dat
-rw-r--r--  1 nielsh  staff     8909 13 Jan 15:57 pathologic.log

just make sure the contents are well formed.

If running the analysis directly on the well-formed MP output doesn't work, we might have to pull in the SRI guys into the mix. They have a pretty good support team for Pathway Tools related issues.

[nielshanson]

Hey, Did you got to the bottom of this? Niels

[sunitj]

Nope. Trying to work it our with the folks at SRI. I'll update this thread as soon as I figure it out. Apologies for the lack of updates.

[sunitj]

It was a permissions issue on my end, SRI also issued a patch to provide a more meaningful error. Here is a portion of the email I received from SRI:

The initial warning, about  "/opt/packages/pathway-tools/data/ptools-local/ptools-init.dat" does not appear to be the cause of the problem, but it is disturbing, and could potentially be symptomatic of other issues.
Regardless, the actual error seems to be being triggered by the empty PGDB-counter.dat file.  That file is automatically created by batch-pathologic if it does not yet exist, but then it is immediately written to, so I'm not sure how it could have ended up empty.  Could there be a permissions issue here too?  I have just issued a patch such that if the file is empty, it is treated the same as if it does not yet exist -- the next time you run pathway-tools that patch should be incorporated automatically.

I checked the permissions, and surely, I had missed changing permissions for /data/ptools-local. I changed this and ran the same command again, only to run into the "This ID already exists" error, I fixed it as described here ran the pipeline again and... Success!

[hallamlab]

Please use the newest version of MP on GitHub