Exception in thread "main" java.lang.reflect.InvocationTargetException

[tseemann]

% bwa mem ref.fa r1.fq r2.fq | samtools sort -o out.cram -O CRAM --reference ref.fa

% cramtools  qstat -I out.cram

Exception in thread "main" java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        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.readSAMFileHeader(CramIO.java:254)
        at htsjdk.samtools.cram.build.CramIO.readCramHeader(CramIO.java:191)
        at net.sf.cram.QualityScoreStats.dist(QualityScoreStats.java:67)
        at net.sf.cram.QualityScoreStats.main(QualityScoreStats.java:61)
        ... 6 more
Caused by: java.lang.ClassNotFoundException: org.apache.commons.compress.utils.CountingOutputStream
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 10 more