java.io.IOException: Stream closed

GitHub | Georgehe4 | 2 weeks ago
  1. 0

    GitHub comment 1340#270263389

    GitHub | 2 weeks 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 | 2 months ago | heuermh
    java.lang.RuntimeException: Piped command List(tee, /dev/null) exited with error code 143.
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  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 | 4 months ago | jpdna
    java.io.FileNotFoundException: Couldn't find any files matching *.adam

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    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