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Daniel-Liu-c0deb0t / UMICollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.
MIT License
62 stars 8 forks source link

java.lang.NoClassDefFoundError: htsjdk/samtools/SamReaderFactory #3

Closed umasstr closed 4 years ago

umasstr commented 4 years ago

EDIT

jarfile curl links are no longer valid. Sorry I missed this. May want to update htsjdk-2.19.0.jar and snappy-java-1.1.7.3.jar links.

Hi Daniel,

I am trying to de-duplicate sorted and indexed bams, but this error is produced with every sample. Thanks for the help. 


~/UMICollapse$ for i in *.sort.bam; do ./umicollapse bam -i $i -o ${i%.sort*}.dup.bam;done

Arguments       [bam, -i, i504_i719_S1.sort.bam, -o, i504_i719_S1.dup.bam]
Exception in thread "main" java.lang.NoClassDefFoundError: htsjdk/samtools/SamReaderFactory
        at umicollapse.main.DeduplicateSAM.deduplicateAndMerge(DeduplicateSAM.java:36)
        at umicollapse.main.Main.main(Main.java:169)
Caused by: java.lang.ClassNotFoundException: htsjdk.samtools.SamReaderFactory
        at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
        at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
        ... 2 more````
Daniel-Liu-c0deb0t commented 4 years ago

I've updated the curl URLs in the readme. Thanks for letting me know!