The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block.
Powered by Vanilla. Made with Bootstrap.
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Consistant error seen in Picard 1.119

datakiddatakid At my deskMember Posts: 3

I have had a couple of enquiries over the last few days wrt this warning message that we are seeing a lot of:

Java HotSpot(TM) 64-Bit Server VM warning: You have loaded library /config/binaries/picard/1.119/libIntelDeflater.so which might have disabled stack guard. The VM will try to fix the stack guard now.
Java HotSpot(TM) 64-Bit Server VM warning: You have loaded library /config/binaries/picard/1.119/libIntelDeflater.so which might have disabled stack guard. The VM will try to fix the stack guard now.
Java HotSpot(TM) 64-Bit Server VM warning: You have loaded library /config/binaries/picard/1.119/libIntelDeflater.so which might have disabled stack guard. The VM will try to fix the stack guard now.

That module is using the locally installed java/1.7.0_80

Is this a problem that was solved in a later version of Picard, is this something I can fix in the 1.119 version, is this something that I need to be worried about (from a results perspective - obv there seems to be an implicit security issue).

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,184 admin
    Not sure what is going on there but I believe the libIntelDeflater was replaced by something else in a recent version, so it's worth trying the latest. You'll need Java 8 for that.

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.