Entering edit mode
7.8 years ago
ttom
▴
220
Using cramtools 3.0
The same error was posted in https://github.com/enasequence/cramtools/issues/55
**cramtools cram -I TEST.bam -R Human_Decoy_REF/hs37d5.fa -O TEST.bam.cram**
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at net.sf.cram.CramTools.invoke(CramTools.java:91)
at net.sf.cram.CramTools.main(CramTools.java:121)
Caused by: java.lang.NoClassDefFoundError: org/apache/commons/compress/utils/CountingOutputStream
at htsjdk.samtools.cram.build.CramIO.writeContainerForSamFileHeader(CramIO.java:247)
at htsjdk.samtools.cram.build.CramIO.writeCramHeader(CramIO.java:161)
at net.sf.cram.Bam2Cram.main(Bam2Cram.java:405)
... 6 more
Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
... 9 more
Why is this happening ? Would appreciate help.
Thanks !!