java.io.IOException: Stream closed

GitHub | Georgehe4 | 2 months ago
tip
Your exception is missing from the Samebug knowledge base.
Here are the best solutions we found on the Internet.
Click on the to mark the helpful solution and get rewards for you help.
  1. 0

    GitHub comment 1340#270263389

    GitHub | 2 months ago | heuermh
    org.apache.parquet.io.ParquetEncodingException: /Users/heuermh/working/adam/sorted.adam/part-r-00000.gz.parquet invalid: all the files must be contained in the root sorted.adam
  2. 0

    GitHub comment 1292#263346229

    GitHub | 3 months ago | heuermh
    java.lang.RuntimeException: Piped command List(tee, /dev/null) exited with error code 143.
  3. Speed up your debug routine!

    Automated exception search integrated into your IDE

  4. 0

    fasta2adam not working?

    Google Groups | 2 years ago | Marek WiewiĆ³rka
    SRR042441.filt.fastq
  5. 0

    How to read glob of multiple parquet Genotype

    GitHub | 5 months ago | jpdna
    java.io.FileNotFoundException: Couldn't find any files matching *.adam

    Not finding the right solution?
    Take a tour to get the most out of Samebug.

    Tired of useless tips?

    Automated exception search integrated into your IDE

    Root Cause Analysis

    1. java.io.IOException

      Stream closed

      at org.apache.hadoop.crypto.CryptoOutputStream.checkStream()
    2. org.apache.hadoop
      CryptoOutputStream.flush
      1. org.apache.hadoop.crypto.CryptoOutputStream.checkStream(CryptoOutputStream.java:250)
      2. org.apache.hadoop.crypto.CryptoOutputStream.flush(CryptoOutputStream.java:237)
      2 frames
    3. Java RT
      DataOutputStream.flush
      1. java.io.FilterOutputStream.flush(FilterOutputStream.java:140)
      2. java.io.DataOutputStream.flush(DataOutputStream.java:123)
      2 frames
    4. org.bdgenomics.adam
      Vcf2ADAM.run
      1. org.bdgenomics.adam.rdd.VCFHeaderUtils$.write(VCFHeaderUtils.scala:75)
      2. org.bdgenomics.adam.rdd.VCFHeaderUtils$.write(VCFHeaderUtils.scala:46)
      3. org.bdgenomics.adam.rdd.MultisampleAvroGenomicRDD.saveMetadata(GenomicRDD.scala:827)
      4. org.bdgenomics.adam.rdd.AvroGenomicRDD.saveAsParquet(GenomicRDD.scala:913)
      5. org.bdgenomics.adam.rdd.AvroGenomicRDD.saveAsParquet(GenomicRDD.scala:883)
      6. org.bdgenomics.adam.cli.Vcf2ADAM.run(Vcf2ADAM.scala:74)
      6 frames
    5. net.fnothaft.gnocchi
      RegressPhenotypes.run
      1. net.fnothaft.gnocchi.cli.RegressPhenotypes.loadGenotypes(RegressPhenotypes.scala:152)
      2. net.fnothaft.gnocchi.cli.RegressPhenotypes.run(RegressPhenotypes.scala:118)
      2 frames
    6. org.bdgenomics.utils
      BDGSparkCommand$class.run
      1. org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:55)
      1 frame
    7. net.fnothaft.gnocchi
      GnocchiMain.main
      1. net.fnothaft.gnocchi.cli.RegressPhenotypes.run(RegressPhenotypes.scala:110)
      2. net.fnothaft.gnocchi.cli.GnocchiMain$.main(GnocchiMain.scala:48)
      3. net.fnothaft.gnocchi.cli.GnocchiMain.main(GnocchiMain.scala)
      3 frames
    8. Java RT
      Method.invoke
      1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      4. java.lang.reflect.Method.invoke(Method.java:498)
      4 frames
    9. Spark
      SparkSubmit.main
      1. org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:731)
      2. org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)
      3. org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)
      4. org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)
      5. org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
      5 frames