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


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,


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$ at Method) at at java.lang.ClassLoader.loadClass( at sun.misc.Launcher$AppClassLoader.loadClass( at java.lang.ClassLoader.loadClass(

dependencies error java bbmap • 559 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by shambyross10
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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:

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, is one suggested alternative.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 22 months ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink written 22 months ago by shambyross10
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