Hello
I've encountered an issue with running the cuffdiff tool on our local
production Galaxy instance.
Specifically when a cummerbund SQLite database is requested as output
then the tool fails with an error:
Creating database ./cummeRbund.sqlite
Error in sqliteSendQuery(con, statement, bind.data) :
error in statement: disk I/O error
Error in sqliteSendQuery(con, statement, bind.data) :
error in statement: disk I/O error
Calls: readCufflinks ... .local -> sqliteGetQuery -> sqliteSendQuery ->
.Call
Execution halted
Our Galaxy is configured to use a LustreFS scratch directory for the
'job_working_directory', which I understand is where each job will have
its own working directory created, and I'm wondering if the SQLite error
above is a manifestation of a general problem with SQLite on LustreFS
(see e.g. the answer to this BioStars question
https://www.biostars.org/p/115452/).
The obvious workaround is to change 'job_working_directory', preferably
just for the cuffdiff tool. Does anyone know if it's possible to do this
i.e. set 'job_working_directory' on a per-tool basis?
(Also, has anyone else seen this specific problem with
cuffdiff/cummerbund/SQLite on their local Galaxy instances?)
Thanks for your help - any suggestions greatly appreciated,
Best wishes
Peter
--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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