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Problems writing file with multithreading #65

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Izar-de-villasante opened this issue Jan 19, 2023 · 1 comment
Open

Problems writing file with multithreading #65

Izar-de-villasante opened this issue Jan 19, 2023 · 1 comment
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@Izar-de-villasante
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When jacusa2 ends calling and has to merge it fails. Usually it just gets stacked and the job keeps on running but las time I got this error:

INFO 00:03:31 Thread 51: Working on contig chrY:59301874-59373565
java.lang.NullPointerException: Cannot invoke "java.io.BufferedWriter.write(String)" because "this.bw" is null
at lib.io.AbstractResultFileWriter.writeLine(AbstractResultFileWriter.java:32)
at lib.io.BEDlikeResultFileWriter.writeHeader(BEDlikeResultFileWriter.java:44)
at lib.worker.WorkerDispatcher.writeOutput(WorkerDispatcher.java:124)
at lib.worker.WorkerDispatcher.run(WorkerDispatcher.java:98)
at lib.util.AbstractTool.run(AbstractTool.java:60)
at jacusa.JACUSA.main(JACUSA.java:96)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:61)
I was reading this thread and maybe it is related:
https://es.stackoverflow.com/questions/432241/exception-in-thread-main-java-lang-nullpointerexception-cannot-invoke-alumno

@piechottam
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Can you please provide your JACUSA2 call?

@piechottam piechottam self-assigned this Jan 19, 2023
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