It seems you have downloaded version 2.2 of the RDP Classifier, but
re-named the file to rdp_classifier-2.0.1.jar. Please re-name the
file to something with 2.2 in the name (preferably
rdp_classifier-2.2.jar), and re-set your RDP_JAR_PATH accordingly.
The assign_taxonomy.py script literally checks the name of the jar
file to determine the version. I know this is a terrible hack, but we
included it as a sanity check.
--Kyle
Hi Kyle, Thanks for replying. The file name is rdp_classifier-2.2.jar; a file search did not find any files with the 2.0.1 suffix. As best as I can determine, the qiime_config file doesn't seem to have any mention of the RDP JAR path. Could you let me know how to re-set the RDP JAR PATH? I'm new to the Linux environment. Thanks, Matt --- On Wed, 5/16/12, Kyle Bittinger <kylebi...@gmail.com> wrote: |
Thanks, Kyle. It's kinda good news / bad news. I modified the .bashrc file and no longer get the error message I had before. However, now I get the following output from the same command. The path I'm using is /home/qiime/qiime_tutorial-v1.4.0/otus2/rep_set. The result is an empty folder titled rdp22_assigned_taxonomy. Any thoughts? Thanks! Matt Traceback (most recent call last): File "/home/qiime/bin/assign_taxonomy.py", line 226, in <module> main() File "/home/qiime/bin/assign_taxonomy.py", line 222, in main result_path=result_path,log_path=log_path) File "/home/qiime/lib/qiime/assign_taxonomy.py", line 375, in __call__ max_memory=max_memory) File "/home/qiime/lib/qiime/pycogent_backports/rdp_classifier.py", line 402, in assign_taxonomy app_result = app(data) File "/software/pycogent-1.5.1-release/lib/python2.7/site-packages/cogent/app/util.py", line 250, in __call__ % (str(exit_status),command) cogent.app.util.ApplicationError: Unacceptable application exit status: 1, command: cd "/home/qiime/qiime_tutorial-v1.4.0/otus2/rep_set/"; java -Xmx1000M -jar "/home/qiime/app/rdp_classifier-2.2.jar" -o "/tmp/RdpAssignments_pUuHj1.txt" -f fixrank -q "/tmp/tmpp46C1SPiXP1WWXeBLpLf.txt" > "/tmp/tmplBOhFgDgffuelIv7apmP.txt" 2> "/tmp/tmpzytUHG4hWv1eGI0qTIT3.txt" qiime@linux:~/qiime_tutorial-v1.4.0/otus2/rep_set$ |
Here's the output from that command. Thanks, Matt qiime@linux:~/qiime_tutorial-v1.4.0/otus2/rep_set$ java -Xmx1000M -jar "/home/qiime/app/rdp_classifier-2.2.jar" -o Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/cli/Options at edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd.<clinit>(ClassifierCmd.java:32) Caused by: java.lang.ClassNotFoundException: org.apache.commons.cli.Options at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) ... 1 more Could not find the main class: edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd. Program will exit. --- On Wed, 5/16/12, Antonio González Peña <antg...@gmail.com> wrote: |
Problem solved! Originally, I had unzipped it in the download file, and copied that to the app folder. Thank you both very much for your suggestions. Best, Matt |