Error: Exception in thread "main" java.io.IOException: Stale file handle

[FelipeMSD]

Dear all,

I'm trying to run Trimmomatic, but for few samples I keep finding this on the error file. Do you have any suggestion of what might be wrong?

Exception in thread "main" java.io.IOException: Stale file handle at java.base/java.io.FileOutputStream.writeBytes(Native Method) at java.base/java.io.FileOutputStream.write(FileOutputStream.java:355) at java.base/java.util.zip.DeflaterOutputStream.deflate(DeflaterOutputStream.java:254) at java.base/java.util.zip.DeflaterOutputStream.write(DeflaterOutputStream.java:212) at java.base/java.util.zip.GZIPOutputStream.write(GZIPOutputStream.java:146) at java.base/sun.nio.cs.StreamEncoder.writeBytes(StreamEncoder.java:233) at java.base/sun.nio.cs.StreamEncoder.implWrite(StreamEncoder.java:303) at java.base/sun.nio.cs.StreamEncoder.implWrite(StreamEncoder.java:281) at java.base/sun.nio.cs.StreamEncoder.write(StreamEncoder.java:125) at java.base/java.io.OutputStreamWriter.write(OutputStreamWriter.java:211) at java.base/java.io.BufferedWriter.flushBuffer(BufferedWriter.java:120) at java.base/java.io.BufferedWriter.write(BufferedWriter.java:233) at java.base/java.io.Writer.write(Writer.java:162) at org.usadellab.trimmomatic.fastq.FastqSerializer.writeRecord(FastqSerializer.java:63) at org.usadellab.trimmomatic.TrimmomaticPE.processSingleThreaded(TrimmomaticPE.java:89) at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:316) at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:555) at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

Kind regards, Felipe

[FelipeMSD]

It was a problem with the cluster I was using. Sorry for the inconvenience.

[Jora1991]

@FelipeMSD Hello, I also encountered the same error on the cluster. Could you please let me know what caused the issue in your case? Do you have any solutions or suggestions for resolving it? Thank you very much.