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 > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for all > things parallel software development, from weekly thought leadership blogs to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > > > > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net > -- "For a successful technology, reality must take precedence over public relations, for nature cannot be fooled." - Richard P. Feynman, Rogers Commission Report 1986 ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
