The org.bdgenomics.adam is one of the Components of the GATK, and I just
download the release version from its github website . However, when I build
a new docker image with spark2.4.5 and scala 2.12.4,It works well and that
makes me confused.
root@master2:~# pyspark
Python 2.7.17 (default,
How are you depending on that org.bdgenomics.adam library? Maybe you're
pulling the 2.11 version of that.
Spark 3 supports only Scala 2.12. This actually sounds like third party
library is compiled for 2.11 or something.
On Fri, Jun 5, 2020 at 11:11 PM charles_cai <1620075...@qq.com> wrote:
> Hi Pol,
>
> thanks for your suggestion, I am going to use Spark-3.0.0 for GPU
> acceleration,so I update the
Hi Pol,
thanks for your suggestion, I am going to use Spark-3.0.0 for GPU
acceleration,so I update the scala to the *version 2.12.11* and the latest
*2.13* ,but the error is still there, and by the way , the Spark version is
*spark-3.0.0-preview2-bin-without-hadoop*
Caused by:
> Hi,
>
> I run the GATK MarkDuplicates in Spark mode and it throws an
> *NoClassDefFoundError: scala/Product$class*. The GATK version is 4.1.7 and
> 4.0.0,the environment is: spark-3.0.0, scala-2.11.12
>
> *GATK commands:*
>
> gatk MarkDuplicatesSpark \
> -I h
Hi,
I run the GATK MarkDuplicates in Spark mode and it throws an
*NoClassDefFoundError: scala/Product$class*. The GATK version is 4.1.7 and
4.0.0,the environment is: spark-3.0.0, scala-2.11.12
*GATK commands:*
gatk MarkDuplicatesSpark \
-I hdfs://master2:9000/Drosophila/output
