The current GATK version is 3.8-0
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!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?


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!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Consistant error seen in Picard 1.119

datakiddatakid At my deskMember

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).

Best Answer

Answers

Sign In or Register to comment.