#59 bbduk.sh fails with error"java.lang.NoSuchMethodError: java.lang.Process.isAlive()Z"

[Eric Blanc]

When reading compressed fastq files, bbduk.sh fails with error:

Exception in thread "main" java.lang.NoSuchMethodError: java.lang.Process.isAlive()Z
    at dna.Data.testExecute(Data.java:1829)
    at dna.Data.BGZIP(Data.java:1517)
    at fileIO.ReadWrite.getGZipOutputStream(ReadWrite.java:533)
    at fileIO.ReadWrite.getOutputStream(ReadWrite.java:382)
    at fileIO.ReadWrite.getOutputStream(ReadWrite.java:344)
    at stream.ReadStreamWriter.<init>(ReadStreamWriter.java:71)
    at stream.ReadStreamByteWriter.<init>(ReadStreamByteWriter.java:18)
    at stream.ConcurrentGenericReadOutputStream.<init>(ConcurrentGenericReadOutputStream.java:38)
    at stream.ConcurrentReadOutputStream.getStream(ConcurrentReadOutputStream.java:71)
    at stream.ConcurrentReadOutputStream.getStream(ConcurrentReadOutputStream.java:35)
    at jgi.BBDuk.spawnProcessThreads(BBDuk.java:1932)
    at jgi.BBDuk.process2(BBDuk.java:1198)
    at jgi.BBDuk.process(BBDuk.java:1094)
    at jgi.BBDuk.main(BBDuk.java:81)

This error occurs when the java run-time environment version is 1.7 or older (the isAlive method appears in 1.8). Reading the BBmap package summary, I was under the impression that 1.7 would be supported. I think that the documentation should be updated to clarify this requirement.

PS: Thanks for your excellent software packages!