New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
adam2vcf fails with -coalesce #735
Comments
I actually just saw this as well, and not sure it's related to coalesce. I get an NPE when using a Maybe a separate issue or some bug in the serializer? val adamGenotypes = adamContext.loadParquetGenotypes("/some/path,adam", projection = Some(Projection(GenotypeField.alternateReadDepth)))
adamGenotypes.take(1)
gives
|
I am not able to reproduce with current git HEAD $ ./bin/adam-submit --version
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using SPARK_SUBMIT=/usr/local/bin/spark-submit
e 888~-_ e e e
d8b 888 \ d8b d8b d8b
/Y88b 888 | /Y88b d888bdY88b
/ Y88b 888 | / Y88b / Y88Y Y888b
/____Y88b 888 / /____Y88b / YY Y888b
/ Y88b 888_-~ / Y88b / Y888b
ADAM version: 0.19.1-SNAPSHOT
Commit: d39b374f0d55a1a931bfd66218588ce3d675e902 Build: 2016-07-06
Built for: Scala 2.10 and Hadoop 2.6.0
$ ./bin/adam-submit vcf2adam adam-core/src/test/resources/small.vcf small.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using SPARK_SUBMIT=/usr/local/bin/spark-submit
$ ./bin/adam-submit adam2vcf -coalesce 1 small.adam small.vcf
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using SPARK_SUBMIT=/usr/local/bin/spark-submit
Jul 6, 2016 2:40:28 PM INFO: org.apache.parquet.hadoop.ParquetInputFormat: Total input paths to process : 1
Jul 6, 2016 2:40:29 PM WARNING: org.apache.parquet.hadoop.ParquetRecordReader: Can not initialize counter due to context is not a instance of TaskInputOutputContext, but is org.apache.hadoop.mapreduce.task.TaskAttemptContextImpl
Jul 6, 2016 2:40:29 PM INFO: org.apache.parquet.hadoop.InternalParquetRecordReader: RecordReader initialized will read a total of 15 records.
Jul 6, 2016 2:40:29 PM INFO: org.apache.parquet.hadoop.InternalParquetRecordReader: at row 0. reading next block
Jul 6, 2016 2:40:29 PM INFO: org.apache.parquet.hadoop.InternalParquetRecordReader: block read in memory in 35 ms. row count = 15 |
Closing as not able to reproduce/issue is old. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
It fails with any coalesce value(1,4,10,etc)
Stacktrace:
The text was updated successfully, but these errors were encountered: