akmorrow13

This looks like https://github.com/bigdatagenomics/adam/issues/1742. What spark/scala version are you running?

Using spark-1.6.3-bin-hadoop2.6, I am not able to reproduce this issue. Have you built Mango for Spark 2?

Mango should run on spark 1 and 2. This error can appear if Mango is compiled for Spark 2 but you are running on Spark 1.6.3. However, I cannot reproduce...

Hi @ssabnis ! Have your run `make prepare` from the mango-python directory? Also, are you running in a virtual environment?

I think this is a Spark versioning issue. You are using Spark 2.3.1, but Mango is pre-built [for Spark 2.2.1](https://github.com/bigdatagenomics/mango/blob/master/pom.xml#L34). More specifically, Spark 2.3.1 uses a new version of py4j...

Spark 2.3.1 uses Parquet 1.10.0 https://github.com/apache/spark/blob/master/pom.xml#L132, so you would have to change to this in the Mango pom as well. Just a warning, Mango has not been tested yet with...

@ssabnis can you please post the errors in github? It is easiest for debugging and issue documentation. ``` self._jvm.org.bdgenomics.adam.rdd.ADAMContext.ADAMContextFromSession(ss._jsparkSession) E TypeError: 'JavaPackage' object is not callable ``` generally means that...

Please take a look at [our readthedocs](https://bdg-mango.readthedocs.io) . Under usage and examples, there is both a python and browser based tool that allow visualization of bam files.

@ssabnis one free dataset that you can access is the [1000 genomes dataset](http://www.internationalgenome.org/category/population/). If you are running on AWS, it is hosted there. You can see Mango's [aws notebook tutorial](https://github.com/bigdatagenomics/mango/blob/master/example-files/notebooks/aws-1000genomes.ipynb)...

Please try ` ./mango-submit --packages org.apache.parquet:parquet-hadoop:1.8.2 -- /user/sm/hg19.17.2bit -genes /user/sm/ensGene.bb -reads /user/sm/chr17.7500000-7515000.sam.adam -variants /user/sm/chr17.adam -show_genotypes `