Closed deFerran closed 4 years ago
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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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
Hello,
I'm getting the following error when trying to run Paleomix:
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.