GATK error

[deFerran]

Hello,

I'm getting the following error when trying to run Paleomix:

Version could not be determined for GenomeAnalysisTK:

Attempted to run command:
    $ java -server -Djava.io.tmpdir=/pool/genomics/xxx/xxxxx/xxxxxxx/xxxxxxxxxx/temp -Djava.awt.headless=true -XX:+UseSerialGC -Xmx2g -jar /home/xxxxxxxx/install/jar_root/GenomeAnalysisTK.jar --version

Program may be broken or a version not supported by the
pipeline; please refer to the PALEOMIX documentation.

    Required:       prior to v4.0.x
    Search string:  ^(?:The Genome Analysis Toolkit \(GATK\) v)?(\d+)\.(\d+)

But when I try to run the command showed above: $ java -server -Djava.io.tmpdir=/pool/genomics/xxx/xxxxx/xxxxxxx/xxxxxxxxxx/temp -Djava.awt.headless=true -XX:+UseSerialGC -Xmx2g -jar /home/xxxxxxxx/install/jar_root/GenomeAnalysisTK.jar --version

I get: 3.8-1-0-gf15c1c3ef

So, I`m not sure why it is not working.

Thank you.

[MikkelSchubert]

Hi,

The error message that you received should have included additional output from running the command shown in the error message. Can you copy/paste that as well?

Best regards, Mikkel

On Wed, Feb 12, 2020 at 5:05 PM VeradeFerran notifications@github.com wrote:

Hello,

I'm getting the following error when trying to run Paleomix:

Version could not be determined for GenomeAnalysisTK:

Attempted to run command: $ java -server -Djava.io.tmpdir=/pool/genomics/xxx/xxxxx/xxxxxxx/xxxxxxxxxx/temp -Djava.awt.headless=true -XX:+UseSerialGC -Xmx2g -jar /home/xxxxxxxx/install/jar_root/GenomeAnalysisTK.jar --version

Program may be broken or a version not supported by the pipeline; please refer to the PALEOMIX documentation.

Required:       prior to v4.0.x
Search string:  ^(?:The Genome Analysis Toolkit \(GATK\) v)?(\d+)\.(\d+)

But when I try to run the command showed above: $ java -server -Djava.io.tmpdir=/pool/genomics/xxx/xxxxx/xxxxxxx/xxxxxxxxxx/temp -Djava.awt.headless=true -XX:+UseSerialGC -Xmx2g -jar /home/xxxxxxxx/install/jar_root/GenomeAnalysisTK.jar --version

I get: 3.8-1-0-gf15c1c3ef

So, I`m not sure why it is not working.

Thank you.

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[deFerran]

Hello Mikkel, I just found out what the problem was. I haven't realized that there was an error log files in "temp" folder. I just check it and it was related to amount of memory available. As I was just testing to see if I had installed Paleomix right, I was trying to run it with little memory/threads. I just increased it and now it is working perfectly. Thank you for your time and for all your work with Paleomix! Best regards, Vera