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dieterich-lab / JACUSA2

New version of JACUSA -> 2.0
GNU General Public License v3.0
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Problems writing file with multithreading #65

Open Izar-de-villasante opened 1 year ago

Izar-de-villasante commented 1 year ago

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 commented 1 year ago

Can you please provide your JACUSA2 call?