Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GATK Picard SortSam/MarkDups Error with Snappy Loading

0

3 comments

  • Avatar
    Louis Bergelson

    Hello,

    I'm not sure what's causing this exactly.   What sort of machines is your cluster using?  I'm assuming they're not x64 machines since the intel libraries also aren't loading.

    I don't know exactly why snappy isn't available but it sounds like it's not available for whatever your system is.  

    You should be able to turn off snappy native compression by providing a system property. 

    -Dsamjdk.snappy.disable=true

    I think that should work around your problem.

    0
    Comment actions Permalink
  • Avatar
    Vishal Patel

    Hello, 

    Thank you for the info, we are using linux based systems that are running on a SLURM scheduler. I asked the cluster team to download snappy as a separate module which can be loaded in as well. However, when both GATK and Snappy are loaded, it still is unable to access the library. I assume it is some authorization error but I'm not sure. 

    With the flag above, would the command look like this: 

    picard --java-options -Dsamjdk.snappy.disable=true SortSam -I $file -O ${file%.bam*}.sorted.bam -SO coordinate

    or like this 

    picard SortSam -Dsamjdk.snappy.disable=true -I $file -O ${file%.bam*}.sorted.bam -SO coordinate
    0
    Comment actions Permalink
  • Avatar
    Louis Bergelson

    So we bundle snappy with Picard and it includes native code for a lot of different platforms.  Do you know if your machines are x86/64 or if they're some sort of ARM machine?  I don't think you'll be able to easily provide your own version of snappy because picard won't be able to locate it.

    It looks like you're using some sort of wrapper script to run picard since you're not just invoking it as java -jar picard.jar.  You'll have to look intto the exact details of that script since it's not something that we provide.  The snappy option has to be provided to the JVM that's running picard, not as an argument to the picard program itself.  So imagine first one is probably the right thing to do if that argument exists in your script.  

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk