Re: [base] Problem with RMAexpress plugin [Was: (no subject)]

[Jari H. <jar...@me...>]

It looks like the result file from RMAExpressConsole is not available 
when the result is stored into the database:

 > /tmp/tomcat6-tomcat6-tmp/RMAExpress plug-in/3983/rma.txt (No such file
 > or directory)

You need to check that the file is created and readable.

Which versions of BASE and RMAexpress are you running? Are you running 
in a linux environment?


Jari


On 2015-03-04 04:33, Ross Chapman wrote:
> Hi all
>
> I am trying to analyse some data from an Affymetrix GeneChip Mouse Gene
> 1.0 ST Array [MoGene-1_0-st-v1] chip using the RMAexpress plugin and the
> CDF file downloaded from Affymetrix.  The analysis fails with an
> exception (below).
>
> Can you advise me of what the underlying problem might be and of any
> potential solution.
>
> Many thanks
>
> Ross Chapman
>
> net.sf.basedb.core.BaseException: Unable to import root bioassay.
> at se.lu.thep.affymetrix.RMAExpress.storeResult(RMAExpress.java:218)
> at
> se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:263)
> at
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116)
> at
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: java.io.FileNotFoundException:
> /tmp/tomcat6-tomcat6-tmp/RMAExpress plug-in/3983/rma.txt (No such file
> or directory)
> at java.io.FileInputStream.open(Native Method)
> at java.io.FileInputStream.<init>(FileInputStream.java:146)
> at java.io.FileInputStream.<init>(FileInputStream.java:101)
> at se.lu.thep.affymetrix.RMAExpress.storeResult(RMAExpress.java:167)
> ... 4 more
>
> --
> Dr Ross Chapman
> Senior Bioinformatician
> MIMR-PHI Institute of Medical Research
> 27-31 Wright Street, Clayton, VIC 3168
> (03) 99024766
>
>
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-- 
"For a successful technology, reality must take precedence over public 
relations, for nature cannot be fooled." - Richard P. Feynman, Rogers 
Commission Report 1986