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AnalyzeCovariates: java.nio.file.NoSuchFileException

I'm not sure if this is related to the prior most recent post in this forum, which featured a similar error with a different tool. I'm using GATK

AnalyzeCovariates appears to run fine -- the output PDF file with charts is generated successfully. This error appears immediately afterwards, as shown below.

Because the PDF is generated, can I assume AnalyzeCovariates ran successfully? If so, this error is purely academic. I'm hoping it doesn't interfere with my pipeline and that I can continue with the PDFs that are outputted.

05:15:10.889 INFO AnalyzeCovariates - ------------------------------------------------------------
05:15:10.890 INFO AnalyzeCovariates - The Genome Analysis Toolkit (GATK) v4.1.1.0
05:15:10.890 INFO AnalyzeCovariates - For support and documentation go to URL
05:15:10.891 INFO AnalyzeCovariates - Executing as REDACTED on Linux v4.4.159-1.el7.elrepo.x86_64 amd64
05:15:10.891 INFO AnalyzeCovariates - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_191-8u191-b12-0ubuntu0.16.04.1-b12
05:15:10.891 INFO AnalyzeCovariates - Start Date/Time: May 15, 2019 5:15:09 AM UTC
05:15:10.891 INFO AnalyzeCovariates - ------------------------------------------------------------
05:15:10.891 INFO AnalyzeCovariates - ------------------------------------------------------------
05:15:10.892 INFO AnalyzeCovariates - HTSJDK Version: 2.19.0
05:15:10.892 INFO AnalyzeCovariates - Picard Version: 2.19.0
05:15:10.901 INFO AnalyzeCovariates - HTSJDK Defaults.COMPRESSION_LEVEL : 2
05:15:10.903 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
05:15:10.903 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
05:15:10.904 INFO AnalyzeCovariates - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
05:15:10.907 INFO AnalyzeCovariates - Deflater: JdkDeflater
05:15:10.909 INFO AnalyzeCovariates - Inflater: JdkInflater
05:15:10.910 INFO AnalyzeCovariates - GCS max retries/reopens: 20
05:15:10.911 INFO AnalyzeCovariates - Requester pays: disabled
05:15:10.912 INFO AnalyzeCovariates - Initializing engine
05:15:10.913 INFO AnalyzeCovariates - Done initializing engine
05:15:13.358 INFO AnalyzeCovariates - Generating csv file '/tmp/AnalyzeCovariates3295549975749447065.csv'
05:15:13.633 INFO AnalyzeCovariates - Generating plots file 'SAMPLE_RG_dedup_AnalyzeCovariates.pdf'
05:15:22.015 INFO AnalyzeCovariates - Shutting down engine
[May 15, 2019 5:15:22 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.AnalyzeCovariates done. Elapsed time: 0.21 minutes.
Exception in thread "Thread-1" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /tmp/Rlib.4430253503005822580
at htsjdk.samtools.util.IOUtil.recursiveDelete(IOUtil.java:1346)
at org.broadinstitute.hellbender.utils.io.IOUtils.deleteRecursively(IOUtils.java:1061)
at org.broadinstitute.hellbender.utils.io.DeleteRecursivelyOnExitPathHook.runHooks(DeleteRecursivelyOnExitPathHook.java:56)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.nio.file.NoSuchFileException: /tmp/Rlib.4430253503005822580
at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
at sun.nio.fs.UnixFileAttributeViews$Basic.readAttributes(UnixFileAttributeViews.java:55)
at sun.nio.fs.UnixFileSystemProvider.readAttributes(UnixFileSystemProvider.java:144)
at sun.nio.fs.LinuxFileSystemProvider.readAttributes(LinuxFileSystemProvider.java:99)
at java.nio.file.Files.readAttributes(Files.java:1737)
at java.nio.file.FileTreeWalker.getAttributes(FileTreeWalker.java:219)
at java.nio.file.FileTreeWalker.visit(FileTreeWalker.java:276)
at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:322)
at java.nio.file.Files.walkFileTree(Files.java:2662)
at java.nio.file.Files.walkFileTree(Files.java:2742)
at htsjdk.samtools.util.IOUtil.recursiveDelete(IOUtil.java:1344)
... 3 more
Using GATK jar /gatk/gatk-package-
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4G -jar /gatk$

Best Answer


  • AdelaideRAdelaideR Member admin

    Hi @bramblepuss

    This error occurs most commonly when a file name, directory name or file path has been incorrectly specified when using the file handling classes of java.nio.file package.

    Is there any chance that there has been a change in your directory or file names?

  • bramblepussbramblepuss Member
    > @AdelaideR said:
    > Hi @bramblepuss
    > This error occurs most commonly when a file name, directory name or file path has been incorrectly specified when using the file handling classes of java.nio.file package.
    > Is there any chance that there has been a change in your directory or file names?

    Yes, specifically the issue looks like this file is missing:

    Caused by: java.nio.file.NoSuchFileException: /tmp/Rlib.4430253503005822580

    I presume this file is generated by GATK during the process. There shouldn't be any change in that directory.

    Can I move forward with the generated PDFs, or should I try to resolve this issue first? The PDFs look just fine.
  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin
    Accepted Answer

    @bramblepuss You should be okay to use the PDFs. It looks like there is a fix going out to resolve this issue soon. Here is a link to this issue.

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