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AnalyzeCovariates exceptions

We are seeing this type of exceptions when running BQSR on our samples.

Exception in thread "Thread-1" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /tmp/Rlib.2419203368861408992
        at htsjdk.samtools.util.IOUtil.recursiveDelete(
Caused by: java.nio.file.NoSuchFileException: /tmp/Rlib.2419203368861408992
        at sun.nio.fs.UnixException.translateToIOException(
        at sun.nio.fs.UnixException.rethrowAsIOException(
        at sun.nio.fs.UnixException.rethrowAsIOException(
        at sun.nio.fs.UnixFileAttributeViews$Basic.readAttributes(
        at sun.nio.fs.UnixFileSystemProvider.readAttributes(
        at sun.nio.fs.LinuxFileSystemProvider.readAttributes(
        at java.nio.file.Files.readAttributes(
        at java.nio.file.FileTreeWalker.getAttributes(
        at java.nio.file.FileTreeWalker.visit(
        at java.nio.file.FileTreeWalker.walk(
        at java.nio.file.Files.walkFileTree(
        at java.nio.file.Files.walkFileTree(
        at htsjdk.samtools.util.IOUtil.recursiveDelete(
        ... 3 more
Using GATK jar /gatk/gatk-package-
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package- AnalyzeCovariates -bqsr  ...

I think you should catch RuntimeIOException in the hellbender code as well, not just IOException.

While the error does not seem to be critical, we have not been able to verify that the propagation of this exception does not break any functionality downstream in the processing.

Best Answer


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