Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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 4.1.1.0.

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.
Runtime.totalMemory()=81264640
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$Basic.readAttributes(UnixFileAttributeViews.java:55)
at sun.nio.fs.UnixFileSystemProvider.readAttributes(UnixFileSystemProvider.java:144)
at sun.nio.fs.LinuxFileSystemProvider.readAttributes(LinuxFileSystemProvider.java:99)
at java.nio.file.Files.readAttributes(Files.java:1737)
at java.nio.file.FileTreeWalker.getAttributes(FileTreeWalker.java:219)
at java.nio.file.FileTreeWalker.visit(FileTreeWalker.java:276)
at java.nio.file.FileTreeWalker.walk(FileTreeWalker.java:322)
at java.nio.file.Files.walkFileTree(Files.java:2662)
at java.nio.file.Files.walkFileTree(Files.java:2742)
at htsjdk.samtools.util.IOUtil.recursiveDelete(IOUtil.java:1344)
... 3 more
Using GATK jar /gatk/gatk-package-4.1.1.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4G -jar /gatk$

Best Answer

Answers

  • 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.

Sign In or Register to comment.