shred.sh error

Question

[GLR]

Hello,

I'm trying to shred some sequences using shred.sh with the following commands:

shred.sh in=full_seq.fa out=full_seq_shred.fa length=100000000 minlength=100000000

with which I consistently get the following error:

Exception in thread "main" java.lang.NoClassDefFoundError: stream/FASTQ
    at jgi.Shred.<init>(Shred.java:60)
    at jgi.Shred.main(Shred.java:41)
Caused by: java.lang.ClassNotFoundException: stream.FASTQ
    at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 2 more

I'm not clear what the error means. I've tried several sizes of shred (down to 100) and supplied different sequences. I've checked paths and have redownloaded BBmap to the latest version, with the same result.

Current BBMap version in use: 38.96

Thank you as always.

Answer 1

[GenoMax]

Did you move any of the files around when you downloaded and uncompressed BBMap package? You also need to make sure that your $PATH includes the directory containing BBMap distribution.

[GLR]

Hi Genomax. No I haven't moved any files around and BBMap is in my path and is callable. We had a huge server malfunction which meant my path was previously pointed to a corrupted BBMap distribution, but I've removed this directory, reference from my path and have refreshed the .bashrc with this new distribution.

[GenoMax]

So are things working now? You can easily install bbmap using conda. This will automatically take care of $PATH etc.

[GLR]

Hi Genomax, no things aren't working at the moment, still got the same error. I can try with Conda and see if that corrects the error. I'll get back to you.

[GLR]

Hi Genomax, installing via conda solved the error. I've no idea what's going wrong with just simply downloading it and putting in the path but I'm guessing it's got something to do with the all the left over corrupted paths from the server breakdown. Thanks for your help!