This is a test version of Biostars. For the public version, visit https://www.biostars.org.
shred.sh error

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.

bbshred bbmap
• 1,658 views • link
updated by GenoMax GenoMax • written by GLR • GLR

1 answer

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.

• 0 views • link
written by GenoMax GenoMax

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.

• 0 views • link
written by GLR • GLR

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

• 0 views • link
written by GenoMax GenoMax

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.

• 0 views • link
written by GLR • 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!

• 0 views • link
written by GLR • GLR

Log in to answer this question.

More posts like this
  • NoClassDefFoundError: htsjdk/samtools/util/IntervalTree
    written by wangxiong • wangxiong
    When I run circm6A (https://github.com/canceromics/circm6a) example code: cd ../.. java -Xmx16g -jar circm6a.jar -ip test_data/HeLa_eluate_rep_1.chr22.bam -input test_data/HeLa_input_rep_1.chr22.bam -r test_data/gencode_chr22.gtf -g test_data/hg38_chr22.fa -o test_data/example_Hela The following …
  • Help with Fastqc error
    written by mink2mink2 • mink2mink2
    Hi, people. $sudo fastqc abc.basecaller.bam -o /mgm_test/ Exception in thread "main" java.lang.NoClassDefFoundError: htsjdk/samtools/SAMFormatException at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:100) at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:129) at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:102) at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316) Caused by: …
  • cramtools Java NoClassDefFoundError
    written by ttom ttom
    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 …
  • Mauve Contig Mover Command Line Error
    written by jlc232 • jlc232
    Hello, I'm encountering the following error when trying to run Mauve Contig Mover to reorder the contigs in a draft genome from the Command line. …
  • the problem when I run vcffilterjs
    written by zengtony743 zengtony743
    I am sorry to post this again separately since i am not quite sure if this is the computer issue or the issue from the …
  • SnpEff error message
    written by eb050187 • eb050187
    I seem to get the same error message when I try to do anything using SnpEff. It seems like other people have addressed this error …
  • snpEFF Database building error
    written by Parimala Devi Parimala Devi
    I am using snpEFF for SNP annotation. I am building my own database. I added genome entry to snpEff's configuration. I'm building the database from …
  • An Error About The Recombination Detection Software Dualbrothers
    written by Ontheway • Ontheway
    <p>Hi, I tried to use the software DualBrothers to detect the recombination breakpoints in a set of genes. I installed the software as the instructions …
  • Forum: Biojava Noclassdeffounderror
    written by Rks • Rks
    Hi All I searched if there is any thread regarding biojava `NoClassDefFoundError`, so here I am creating one. I am doing multiple sequence alignment using …
  • How To Get Picard-1.33 Working
    written by Biomed Biomed
    <p>I downloaded Picard-1.33 and I can't seem to get it working under a unix command line. Any help in how you should start this program …