Open JDK 1.8 or Oracle Java 1.8 for Tassel 5 ?

[Willmar Leiser]

I am running the GBS pipeline using Tassel 4 on our Linux server which runs Scientific Linux. Tassel 4 uses Java 1.7, which runs well for all plugins in the GBS pipeline.
Since Tassel 5 is now under current development and also gives some more options, I am very much interested in running Tassel 5. I have Tassel 5.2.10, hence the most recent update, I believe. I can run the FastqToTagCountPlugin, MergeMultipleTagCountPlugin, align the reads tags with BWA, convert the sam file using the SAMConverterPlugin, but then the FastqToTBTPlugin gives me only 0 tags as ouput. There is some heap.size error for java appearing, but I have my heap size at 40GB, which should be sufficient for 570 samples. Since it runs in Tassel4, I assume its a bug in Tassel 5 or its based on the Java version we are using. We have the Open JDK1.8 installed. Do you use the Oracle Java 1.8 version for development, or is that error due to another issue.
Before we will change the servers to Oracle Java, we wanted to make sure it will run afterwards.
Thanks
Willmar

[Lynn Carol Johnson]

Tassel 5 requires Java 1.8

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[Willmar Leiser]

Hi
Yes, its explained that it needs Java 1.8 to run. But my question was rather does it need the original oracle java version or can we also use the open java version for linux called Open JDK 1.8
I had once a similar problem with another program therefore I am asking specifically for the Ipen JDK vs Oracle Java version.
Thanks

[Terry Casstevens]

Hi Willmar,

I don't know if there are issues with Open JDK 1.8. We only use the
Oracle releases. See this document for how to send more information
about Tassel errors.

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf

Best,

Terry

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[Edward S. Buckler]

This would suggest that they should be virtually identical.

http://stackoverflow.com/questions/25936712/what-is-the-difference-between-oracle-jdk-8-and-open-jdk-8

But let us know if this isn’t true.

Cheers-

Ed

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[Willmar Leiser]

Hi Terry and Ed,
I ran it again using now the SeqToTBTHDF5Plugin instead of the FastqToTBTPlugin, now it runs. I guess I am using this plugin now. In tassel 4 both Plugins run smoothly. But will send you the debug report from Tassel 5 anyway. Maybe its of help.
regards
Willmar