Exception when searching with blat

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Exception when searching with blat

kkarimi

Hi all,

 

When attempting to search with blat, I get the following exception:

 

Nov 24, 2014 2:33:01 PM org.apache.catalina.core.StandardWrapperValve invoke

SEVERE: Servlet.service() for servlet [org.bbop.apollo.web.AnnotationEditorService] in context with path [/webApollo] threw exception [Servlet execution threw an exception] with root cause

java.lang.NoSuchMethodError: org.bbop.apollo.tools.seq.search.SequenceSearchTool.search(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)Ljava/util/Collection;

        at org.bbop.apollo.web.AnnotationEditorService.searchSequence(AnnotationEditorService.java:1829)

        at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:771)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)

        at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)

        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)

        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)

        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)

        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)

        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)

        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:931)

        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)

 

It is complaining about an unknown method. What could be wrong?

 

Thanks.

 

-Kamran

 

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Re: Exception when searching with blat

nathandunn

In your config.xml, what do you have in the sequence_search_tool section.  This is mine.  My guess is another (or no class) got instantiated:


<!-- tools to be used for sequence searching.  This is optional.
If this is not setup, WebApollo will not have sequence search support -->
<sequence_search_tools>

   <!-- one <sequence_search_tool> element per tool -->
   <sequence_search_tool>

      <!-- display name for the search tool -->
      <key>BLAT nucleotide</key>

      <!-- class for handling search -->
      <class>org.bbop.apollo.tools.seq.search.blat.BlatCommandLineNucleotideToNucleotide</class>

      <!-- configuration for search tool -->
      <config>/config/blat_config.xml</config>

   </sequence_search_tool>

   <sequence_search_tool>

      <!-- display name for the search tool -->
      <key>BLAT protein</key>

      <!-- class for handling search -->
      <class>org.bbop.apollo.tools.seq.search.blat.BlatCommandLineProteinToNucleotide</class>

      <!-- configuration for search tool -->
      <config>/config/blat_config.xml</config>

   </sequence_search_tool>

</sequence_search_tools>

<!-- data adapters for writi


> On Nov 24, 2014, at 4:25 PM, Kamran Karimi <[hidden email]> wrote:
>
> Hi all,
>  
> When attempting to search with blat, I get the following exception:
>  
> Nov 24, 2014 2:33:01 PM org.apache.catalina.core.StandardWrapperValve invoke
> SEVERE: Servlet.service() for servlet [org.bbop.apollo.web.AnnotationEditorService] in context with path [/webApollo] threw exception [Servlet execution threw an exception] with root cause
> java.lang.NoSuchMethodError: org.bbop.apollo.tools.seq.search.SequenceSearchTool.search(Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)Ljava/util/Collection;
>         at org.bbop.apollo.web.AnnotationEditorService.searchSequence(AnnotationEditorService.java:1829)
>         at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:771)
>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
>         at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
>         at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
>         at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
>         at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)
>         at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
>         at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
>         at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
>         at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
>         at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
>         at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
>         at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
>         at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:931)
>         at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
>  
> It is complaining about an unknown method. What could be wrong?
>  
> Thanks.
>  
> -Kamran


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RE: Exception when searching with blat

kkarimi
In reply to this post by kkarimi

Hi Nathan,

 

Thanks for the response. My config.xml file seems to match yours. I’ve provided the relevant section below. I’ve also copied my blat_config.xml file in this email. I also double checked the permission on the files and directories mentioned in blat_config.xml. Please let me know if I should check anything else.

 

Config.xml snippet:

 

        <sequence_search_tools>

 

                <!-- one <sequence_search_tool> element per tool -->

                <sequence_search_tool>

 

                        <!-- display name for the search tool -->

                        <key>BLAT nucleotide</key>

 

                        <!-- class for handling search -->

                        <class>org.bbop.apollo.tools.seq.search.blat.BlatCommandLineNucleotideToNucleotide</class>

 

                        <!-- configuration for search tool -->

                        <config>/config/blat_config.xml</config>

 

                </sequence_search_tool>

 

                <sequence_search_tool>

 

                        <!-- display name for the search tool -->

                        <key>BLAT protein</key>

 

                        <!-- class for handling search -->

                        <class>org.bbop.apollo.tools.seq.search.blat.BlatCommandLineProteinToNucleotide</class>

 

                        <!-- configuration for search tool -->

                        <config>/config/blat_config.xml</config>

 

                </sequence_search_tool>

 

        </sequence_search_tools>

 

 

 

Blat_config.xml :

<?xml version="1.0" encoding="UTF-8"?>

 

<!-- configuration file for setting up command line Blat support -->

 

<blat_config>

 

        <!-- path to Blat binary -->

        <blat_bin>/usr/bin/blat</blat_bin>

 

        <!-- path to where to put temporary data -->

        <tmp_dir>/data2/webapollo/blat/tmp</tmp_dir>

 

        <!-- path to Blat database -->

        <database>/data2/webapollo/blat/db/genomic.2bit</database>

 

        <!-- any Blat options (directly passed to Blat) e.g., -minMatch -->

        <blat_options></blat_options>

 

        <!-- true to remove temporary data path after search (set to false for debugging purposes) -->

        <remove_tmp_dir>false</remove_tmp_dir>

 

</blat_config>

 

-Kamran

 

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Re: Exception when searching with blat

nathandunn

Hmm . . my next question would be what version of the code are you using?  

The only other likely scenario is that you somehow have two versions merged in together.  

Nathan

On Nov 25, 2014, at 1:22 PM, Kamran Karimi <[hidden email]> wrote:

Hi Nathan,
 
Thanks for the response. My config.xml file seems to match yours. I’ve provided the relevant section below. I’ve also copied my blat_config.xml file in this email. I also double checked the permission on the files and directories mentioned in blat_config.xml. Please let me know if I should check anything else.
 
Config.xml snippet:
 
        <sequence_search_tools>
 
                <!-- one <sequence_search_tool> element per tool -->
                <sequence_search_tool>
 
                        <!-- display name for the search tool -->
                        <key>BLAT nucleotide</key>
 
                        <!-- class for handling search -->
                        <class>org.bbop.apollo.tools.seq.search.blat.BlatCommandLineNucleotideToNucleotide</class>
 
                        <!-- configuration for search tool -->
                        <config>/config/blat_config.xml</config>
 
                </sequence_search_tool>
 
                <sequence_search_tool>
 
                        <!-- display name for the search tool -->
                        <key>BLAT protein</key>
 
                        <!-- class for handling search -->
                        <class>org.bbop.apollo.tools.seq.search.blat.BlatCommandLineProteinToNucleotide</class>
 
                        <!-- configuration for search tool -->
                        <config>/config/blat_config.xml</config>
 
                </sequence_search_tool>
 
        </sequence_search_tools>
 
 
 
Blat_config.xml :
<?xml version="1.0" encoding="UTF-8"?>
 
<!-- configuration file for setting up command line Blat support -->
 
<blat_config>
 
        <!-- path to Blat binary -->
        <blat_bin>/usr/bin/blat</blat_bin>
 
        <!-- path to where to put temporary data -->
        <tmp_dir>/data2/webapollo/blat/tmp</tmp_dir>
 
        <!-- path to Blat database -->
        <database>/data2/webapollo/blat/db/genomic.2bit</database>
 
        <!-- any Blat options (directly passed to Blat) e.g., -minMatch -->
        <blat_options></blat_options>
 
        <!-- true to remove temporary data path after search (set to false for debugging purposes) -->
        <remove_tmp_dir>false</remove_tmp_dir>
 
</blat_config>
 
-Kamran

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RE: Exception when searching with blat

kkarimi
In reply to this post by kkarimi

It turned out to be an incompatibility between the class and jar files in my 2014-04-03 installation. I am not sure how that happened, but installing WebApollo-1.0.2 removed the problem and now blat is functioning.

 

Thanks Nathan for your great help in resolving this issue!

 

-Kamran