Question: BBMap NoClass Error
0
gravatar for shambyross
10 months ago by
shambyross10
shambyross10 wrote:

Hello.

I am running the following (see below) in mac terminal as indicated by biostar handbook for proper BBMap installation. Then, I get the error lang.NoClassDefFoundError: in=reads/fq.

Can anyone help me to understand and resolve the problem?

Thank you,

Ross

java -Xmx2g -cp /Users/rossshamby/src/bbmap/current/align2.BBMap in=reads.fq out=mapped.sam

Exception in thread "main" java.lang.NoClassDefFoundError: in=reads/fq Caused by: java.lang.ClassNotFoundException: in=reads.fq at java.net.URLClassLoader$1.run(URLClassLoader.java:202) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:190) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:247)

dependencies error java bbmap • 257 views
ADD COMMENTlink modified 10 months ago by Jennifer Hillman Jackson23k • written 10 months ago by shambyross10
0
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

This is very similar to a problem another person had with this tool suite. The solution was to verify and enforce the use of the correct Java version required by the tool: https://www.biostars.org/p/199377/

This was mentioned earlier in a reply to your prior post, but it is still true - this forum is for Galaxy-specific questions. For general bioinformatics questions unrelated to Galaxy, https://www.biostars.org/ is one suggested alternative.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 10 months ago by Jennifer Hillman Jackson23k

sorry, Jen - next time will go to Java forum. Can I ask questions relevant to bioinformatics tools here - not necessarily galaxy?

ADD REPLYlink written 10 months ago by shambyross10
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