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Question: BBMap NoClass Error
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gravatar for shambyross
22 months ago by
shambyross • 10
shambyross • 10 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 • 559 views
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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by shambyross • 10
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gravatar for Jennifer Hillman Jackson
22 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 22 months ago by shambyross • 10
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