One source for the problem is that the underlying RMAExpressConsole program doesn't handle ST arrays, or maybe treats ST arrays differently. Have you checked with the author of RMAExpress tool?
The se.lu.thep.affymetrix for BASE plug-in and expects the output file from RMAExpressConsole to be rma.txt. Either RMAExpressConsole crashes or does not create rma.txt but rather something else. I cannot test anything myself since we do not have any ST array data nor a running BASE 2 server (which is required for the affymetrix plug-in). I suggest that you try to run RMAExpressConsole manually on your server and see what the outcome is. Are ST arrays accepted by RMAExpressConsole, does RMAExpressConsole crash (this should be caught by the plug-in), is another set of output files created for ST arrays? (Another thing to check is what files and directories are created by the plug-in once it is finished but unfortunately this is harder to accomplish since the affymetrix plug-in cleans up after it finishes.) Jari On 2015-03-11 01:01, Ross Chapman wrote: > Hi Jari > > Thank you for your comments. > > I am using BASE 2.17.2 which is running on a Linux/Ubuntu server. > > I have found that RMAExpress runs perfectly with most Affymetrix files, > but I get this error when analysing data from Affymetrix GeneChip Human > Gene 1.0 ST or Affymetrix GeneChip Mouse Gene 1.0 ST arrays, so I > believe that the error must lie with the configuration of the ST arrays > within base. > > I preloaded the probes as reporters into the database from a cdf file > for each array, and the reporters are visible in the database. > > Yet somehow the RMAExpress plugin is failing with these arrays. > > I would appreciate any comments or suggestions. > > Thanks > > Ross > > On 5 March 2015 at 00:18, <basedb-users-requ...@lists.sourceforge.net > <mailto:basedb-users-requ...@lists.sourceforge.net>> wrote: > > Send basedb-users mailing list submissions to > basedb-users@lists.sourceforge.net > <mailto:basedb-users@lists.sourceforge.net> > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/basedb-users > or, via email, send a message with subject or body 'help' to > basedb-users-requ...@lists.sourceforge.net > <mailto:basedb-users-requ...@lists.sourceforge.net> > > You can reach the person managing the list at > basedb-users-ow...@lists.sourceforge.net > <mailto:basedb-users-ow...@lists.sourceforge.net> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of basedb-users digest..." > > Today's Topics: > > 1. Re: BASE reporter fields problem (Nicklas Nordborg) > 2. BASE 3.4 has been released (Nicklas Nordborg) > 3. RMAexpress (Ross Chapman) > 4. Re: RMAexpress (Jari H?kkinen) > 5. BASE 3.4.1 has been released (Nicklas Nordborg) > 6. (no subject) (Ross Chapman) > 7. Re: Problem with RMAexpress plugin [Was: (no subject)] > (Jari H?kkinen) > > > ---------- Forwarded message ---------- > From: Nicklas Nordborg <nicklas.nordb...@med.lu.se > <mailto:nicklas.nordb...@med.lu.se>> > To: BASE ML <basedb-users@lists.sourceforge.net > <mailto:basedb-users@lists.sourceforge.net>> > Cc: > Date: Mon, 12 Jan 2015 07:50:46 +0100 > Subject: Re: [base] BASE reporter fields problem > On 2015-01-12 07:25, Ross Chapman wrote: > > Hi all > > I recently moved a BASE2 database to a new server by copying the > full > database and all installation files along with plugin files. > > When I try to run some custom plugins on the new instance, I > receive an > error stating that there is an unknown reporter field being > requested in > the new database version. The same plugins still work fine on the > original BASE2 application. > > Can you point me to where the reporter fields are set and how I can > correct the annotations in the new instance. > > > This should be in the extended-properties.xml file that is found in > the WEB-INF/classes directory in your BASE installation. See > > http://base.thep.lu.se/chrome/__site/latest/html/appendix/__extendedproperties.html > > <http://base.thep.lu.se/chrome/site/latest/html/appendix/extendedproperties.html> > for some more information. > > /Nicklas > > > > > > ---------- Forwarded message ---------- > From: Nicklas Nordborg <nicklas.nordb...@med.lu.se > <mailto:nicklas.nordb...@med.lu.se>> > To: BASE ML <basedb-users@lists.sourceforge.net > <mailto:basedb-users@lists.sourceforge.net>>, BASE dev > <basedb-de...@lists.sourceforge.net > <mailto:basedb-de...@lists.sourceforge.net>>, > <basedb-annou...@lists.sourceforge.net > <mailto:basedb-annou...@lists.sourceforge.net>> > Cc: > Date: Wed, 14 Jan 2015 14:41:58 +0100 > Subject: [base] BASE 3.4 has been released > Hello all, > > After fixing a few issues with the beta version, BASE 3.4.0 has now > been released. One new feature is the possibility to install skins. > Check out the example skins at > http://baseplugins.thep.lu.se/__wiki/net.sf.basedb.__skincollection > <http://baseplugins.thep.lu.se/wiki/net.sf.basedb.skincollection> > > For a complete list of changes, see: > http://base.thep.lu.se/query?__milestone=BASE+3.4&group=type > <http://base.thep.lu.se/query?milestone=BASE+3.4&group=type> > > Installation/upgrade instructions: > http://base.thep.lu.se/chrome/__site/latest/html/admin/__installation.html > <http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html> > > As usual, the program can be downloaded from: > http://base.thep.lu.se/wiki/__DownloadPage > <http://base.thep.lu.se/wiki/DownloadPage> > > /Nicklas > > > > > ---------- Forwarded message ---------- > From: Ross Chapman <ross.chap...@mimr-phi.org > <mailto:ross.chap...@mimr-phi.org>> > To: basedb-users@lists.sourceforge.net > <mailto:basedb-users@lists.sourceforge.net> > Cc: > Date: Tue, 3 Feb 2015 16:55:30 +1100 > Subject: [base] RMAexpress > Hi all > > I am having problems running the RMAexpress plug in after migrating > BASE2 to a new server. > > > The plug in fails with the following error: > > java.io.IOException: Unexpected exit of RMAExpress sub-process. > Return value: 127 > at se.lu.thep.affymetrix.RMAExpress.runBinary(RMAExpress.java:156) > at > > se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:262) > at > > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116) > at > > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510) > at java.lang.Thread.run(Thread.java:745) > > Can you suggest a possible cause and solution? > > Many thanks > > Ross > > -- > Dr Ross Chapman > Senior Bioinformatician > MIMR-PHI Institute of Medical Research > 27-31 Wright Street, Clayton, VIC 3168 > (03) 99024766 > > > ---------- Forwarded message ---------- > From: "Jari Häkkinen" <jari.hakki...@med.lu.se > <mailto:jari.hakki...@med.lu.se>> > To: basedb-users@lists.sourceforge.net > <mailto:basedb-users@lists.sourceforge.net> > Cc: > Date: Tue, 03 Feb 2015 14:20:45 +0100 > Subject: Re: [base] RMAexpress > Hi, > > Did you also move the underlying RMAexpress binary to the new > server? You probably need to recompile RMAExpress > (http://rmaexpress.bmbolstad.__com/ > <http://rmaexpress.bmbolstad.com/>) for your new server. > > > Jari > > > On 2015-02-03 06:55, Ross Chapman wrote: > > Hi all > > I am having problems running the RMAexpress plug in after migrating > BASE2 to a new server. > > > The plug in fails with the following error: > > java.io.IOException: Unexpected exit of RMAExpress sub-process. > Return > value: 127 > at > se.lu.thep.affymetrix.__RMAExpress.runBinary(__RMAExpress.java:156) > at > > se.lu.thep.affymetrix.__AbstractExternalBinaryPlugin.__run(__AbstractExternalBinaryPlugin.__java:262) > at > > net.sf.basedb.core.__PluginExecutionRequest.invoke(__PluginExecutionRequest.java:__116) > at > > net.sf.basedb.core.__InternalJobQueue$JobRunner.__run(InternalJobQueue.java:510) > at java.lang.Thread.run(Thread.__java:745) > > Can you suggest a possible cause and solution? > > Many thanks > > Ross > > -- > 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/ > <http://goparallel.sourceforge.net/> > > > > _________________________________________________ > The BASE general discussion mailing list > basedb-users@lists.__sourceforge.net > <mailto:basedb-users@lists.sourceforge.net> > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-request@lists.__sourceforge.net > <mailto: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 > > > > > ---------- Forwarded message ---------- > From: Nicklas Nordborg <nicklas.nordb...@med.lu.se > <mailto:nicklas.nordb...@med.lu.se>> > To: <basedb-annou...@lists.sourceforge.net > <mailto:basedb-annou...@lists.sourceforge.net>>, BASE ML > <basedb-users@lists.sourceforge.net > <mailto:basedb-users@lists.sourceforge.net>>, BASE dev > <basedb-de...@lists.sourceforge.net > <mailto:basedb-de...@lists.sourceforge.net>> > Cc: > Date: Tue, 10 Feb 2015 13:06:18 +0100 > Subject: [base] BASE 3.4.1 has been released > Hello all, > > We have released BASE 3.4.1 today. This is a bugfix release that > fixes a few minor problems. > > For a complete list of changes, see: > http://base.thep.lu.se/query?__milestone=BASE+3.4.1&group=__type > <http://base.thep.lu.se/query?milestone=BASE+3.4.1&group=type> > > Installation/upgrade instructions: > http://base.thep.lu.se/chrome/__site/latest/html/admin/__installation.html > <http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html> > > As usual, the program can be downloaded from: > http://base.thep.lu.se/wiki/__DownloadPage > <http://base.thep.lu.se/wiki/DownloadPage> > > /Nicklas > > > > > ---------- Forwarded message ---------- > From: Ross Chapman <ross.chap...@mimr-phi.org > <mailto:ross.chap...@mimr-phi.org>> > To: basedb-users@lists.sourceforge.net > <mailto:basedb-users@lists.sourceforge.net> > Cc: > Date: Wed, 4 Mar 2015 14:33:04 +1100 > Subject: [base] (no subject) > 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 > > > ---------- Forwarded message ---------- > From: "Jari Häkkinen" <jari.hakki...@med.lu.se > <mailto:jari.hakki...@med.lu.se>> > To: basedb-users@lists.sourceforge.net > <mailto:basedb-users@lists.sourceforge.net> > Cc: > Date: Wed, 04 Mar 2015 14:18:16 +0100 > Subject: Re: [base] Problem with RMAexpress plugin [Was: (no subject)] > 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/ > <http://goparallel.sourceforge.net/> > > > > _________________________________________________ > The BASE general discussion mailing list > basedb-users@lists.__sourceforge.net > <mailto:basedb-users@lists.sourceforge.net> > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-request@lists.__sourceforge.net > <mailto: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/ > _______________________________________________ > basedb-users mailing list > basedb-users@lists.sourceforge.net > <mailto:basedb-users@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/basedb-users > > > > > -- > 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
