Skip to content
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

Issue with adam2vcf #1787

Closed
Rokshan2016 opened this Issue Oct 30, 2017 · 1 comment

Comments

Projects
3 participants
@Rokshan2016
Copy link

Rokshan2016 commented Oct 30, 2017

Hi,

I am using this command - ./adam-submit --driver-memory 3g --executor-memory 3g -- adam2vcf -single hdfs://ipsawdvpvfhnn03.ips.local:8020/user/rokshan.jahan/avocado_data/SRR1517974.adam hdfs://ipsawdvpvfhnn03.ips.local:8020/user/rokshan.jahan/SRR1517974.vcf -sort_on_save

SRR1517974.adam - this file I got using avocado biallelicgenotyper

Error-

Oct 30, 2017 2:49:45 PM INFO: org.apache.parquet.hadoop.InternalParquetRecordReader: block read in memory in 153 ms. row count = 1
Oct 30, 2017 2:49:45 PM IN17/10/30 14:49:45 INFO Executor: Finished task 16.0 in stage 0.0 (TID 16). 1278 bytes result sent to driver
17/10/30 14:49:45 INFO TaskSetManager: Starting task 17.0 in stage 0.0 (TID 17, localhost, executor driver, partition 17, ANY, 6146 bytes)
17/10/30 14:49:45 INFO Executor: Running task 17.0 in stage 0.0 (TID 17)
17/10/30 14:49:45 INFO NewHadoopRDD: Input split: ParquetInputSplit{part: hdfs://ipsawdvpvfhnn03.ips.local:8020/user/rokshan.jahan/avocado_data/SRR1517974.adam/part-r-00017.gz.parquet start: 0 end: 32528 length: 32528 hosts: []}
17/10/30 14:49:45 INFO TaskSetManager: Finished task 6.0 in stage 0.0 (TID 6) in 676 ms on localhost (executor driver) (1/200)
17/10/30 14:49:45 INFO TaskSetManager: Finished task 16.0 in stage 0.0 (TID 16) in 49 ms on localhost (executor driver) (2/200)
17/10/30 14:49:45 INFO CodecPool: Got brand-new decompressor [.gz]
17/10/30 14:49:45 ERROR Executor: Exception in task 8.0 in stage 0.0 (TID 8)
java.lang.ClassCastException: java.lang.Double cannot be cast to java.lang.Float
at org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:80)
at org.apache.avro.generic.GenericDatumWriter.writeArray(GenericDatumWriter.java:138)
at org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:68)
at org.apache.avro.generic.GenericDatumWriter.writeField(GenericDatumWriter.java:114)
at org.apache.avro.generic.GenericDatumWriter.writeRecord(GenericDatumWriter.java:104)
at org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:66)
at org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:58)

Any suggestion will be helpful for this issue.

Thanks

@fnothaft fnothaft added the wontfix label Jan 9, 2018

@fnothaft

This comment has been minimized.

Copy link
Member

fnothaft commented Jan 9, 2018

Hi @Rokshan2016! This error means that you were running on a Parquet file that had an older schema than your current build of ADAM. Closing for now.

@fnothaft fnothaft closed this Jan 9, 2018

@heuermh heuermh added this to the 0.24.0 milestone Jan 9, 2018

@heuermh heuermh added this to Completed in Release 0.24.0 Feb 10, 2018

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.