java version compatible with GATK 3.2.2

Question

[shpak.max]

I'm working with an old alignment/variant calling pipeline that uses UnifiedGenotyper on GATK v. 3.2.2, which is no longer supported by GATK (I'm stuck with this because we want our new alignments and variant calls to be consistent with those made years ago).

Sometime in the last year, one of the java updates was to a version that is evidently incompatible with GATK 3.2.2, because for various GATK 3.2.2 functions that had previously worked on the server, I get the error e.g.

ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: UnifiedGenotyper

(I get the same issue with RealignerTargetCreator, so presumably nothing on GATK 3 will work with the current java).

The problem is, I don't recall the most recent version of java that would run GATK 3.2.2. The current java on the machine is 11.0.20, so obviously it would have to be something older than that.

Does anybody know what java version I would need to run GATK 3.2?

[Pierre Lindenbaum]

Does anybody know what java version I would need to run GATK 3.2?

should be java 1.8

[shpak.max]

Thanks. Just to follow-up, GATK 3.2.2 will not run on any more recent version, correct?

Answer 1

[LChart]

The conda recipe has restrictions for JDK >=8 and < 9; so try one of the v8 versions.

[shpak.max]

Thanks, but I don't see 3.2.2 listed in the link, only more recent GATK 3. Hopefully 1.8 will work with 3.2.2, I believe this may have been the jdk version that was previously on the server when I last ran 3.2.2 a couple of years ago

[shpak.max]

I tried running GATK 3.2.2 with amazon docker java v. 8, and rather than getting the "Malformed Walker argument", I get an "Unable to access jarfile GenomeAnalysisTK.jar" error. With the new version of java, at least the GATK.jar is recognized but not its downstream functions, whereas it seems like with docker java 8 not even the jar file is readable. Do you have any idea of what may be going on?

[Pierre Lindenbaum]

show us the command line please.

[shpak.max]

I'm in the directory containing the GenomeAnalysisTK.jar file. If I use the version of java installed on the server (java 11.0.20)

java -Xmx5g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper

I get the error "ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: UnifiedGenotyper", i.e. so at least the jar file is recognized.

If I attempt to use the amazon docker java 8, i.e.

docker run amazoncorretto:8 java -Xmx5g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper

the error I get is "Error: Unable to access jarfile GenomeAnalysisTK.jar", so unlike the newer version of java, this one doesn't even recognize the jarfile.

On the GATK forum, someone mentioned that GATK 3.2.2 originally ran on 1.7 and couldn't speak to whether it would work on 1.8, but I find the fact that 8 can't even recognize the jar file while 11 can troubling.