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ucagenomix / sicelore-2.1

MIT License
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java.lang.InterruptedException #16

Closed xuzhougeng closed 7 months ago

xuzhougeng commented 7 months ago

I applied the following version of Java to do the first step of data processing, but encountered the following error report.

$ java -version
openjdk version "21.0.1-internal" 2023-10-17
OpenJDK Runtime Environment (build 21.0.1-internal-adhoc.conda.src)
OpenJDK 64-Bit Server VM (build 21.0.1-internal-adhoc.conda.src, mixed mode, sharing)

The error message:

Nov 06, 2023 5:43:16 PM com.rw.nanoporereadscanner.readerwriter.FastqWriterThreadPool$FastQoneFileThread addChunk
SEVERE: null
java.lang.InterruptedException
    at java.base/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:1722)
    at java.base/java.util.concurrent.LinkedBlockingDeque.putLast(LinkedBlockingDeque.java:389)
    at java.base/java.util.concurrent.LinkedBlockingDeque.put(LinkedBlockingDeque.java:642)
    at com.rw.nanoporereadscanner.readerwriter.FastqWriterThreadPool$FastQoneFileThread.addChunk(FastqWriterThreadPool.java:255)
    at com.rw.nanoporereadscanner.readerwriter.FastqWriterThreadPool.addChunkToThread(FastqWriterThreadPool.java:137)
    at com.rw.nanoporereadscanner.WorkerReadscanner$JobDoneCallBack.onSuccess(WorkerReadscanner.java:324)
    at com.rw.nanoporereadscanner.WorkerReadscanner$JobDoneCallBack.onSuccess(WorkerReadscanner.java:313)
    at com.google.common.util.concurrent.Futures$CallbackListener.run(Futures.java:1133)
    at java.base/java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1423)
    at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:387)
    at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1312)
    at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1843)
    at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1808)
    at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:188)

This is my command,

java -Xmx40g -jar sicelore-2.1/Jar/NanoporeBC_UMI_finder-2.1.jar  scanfastq -d data2/ -o $PWD/result2 --bcEditDistance 1

Could you give me some advice to solve this problem?

xuzhougeng commented 7 months ago

It was solved by using JAVA 17