search

broadinstitute / picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
https://broadinstitute.github.io/picard/
MIT License
983 stars 369 forks source link

Exception in thread "main" java.lang.IllegalStateException: Shutdown in progress #1818

Closed CherryX727 closed 1 year ago

CherryX727 commented 2 years ago

Hi， Thank you for your contribution to picard tools.But when I try to use Picard ​FastqToSam the following error has occurred and I wonder how to solve this problem.

picard.sam.FastqToSam done. Elapsed time: 26.47 minutes.
Runtime.totalMemory()=11863064576
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalStateException: Shutdown in progress
        at htsjdk.samtools.util.nio.DeleteOnExitPathHook.add(DeleteOnExitPathHook.java:39)
        at htsjdk.samtools.util.IOUtil.deleteOnExit(IOUtil.java:434)
        at htsjdk.samtools.util.IOUtil.newTempPath(IOUtil.java:397)
        at htsjdk.samtools.util.SortingCollection.newTempFile(SortingCollection.java:278)
        at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:249)
        at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:182)
        at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:187)
        at picard.sam.FastqToSam.doPaired(FastqToSam.java:414)
        at picard.sam.FastqToSam.makeItSo(FastqToSam.java:380)
        at picard.sam.FastqToSam.doWork(FastqToSam.java:353)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

The code I used to run this project as the following.

java -jar picard.jar FastqToSam -FASTQ /home/data/software/DropSeq_tools/test_data/SRR1748411_1.fastq.gz \
                                -FASTQ2 /home/data/software/DropSeq_tools/test_data/SRR1748411_2.fastq.gz \
                                -OUTPUT /home/data/software/DropSeq_tools/test_data/SRR1748411.bam \
                                -SAMPLE_NAME GSM1544798

Thanks for your answer.

kockan commented 1 year ago

Closing this issue for now due to the amount of time passed since the open date. Feels like a bit more info was needed for proper debugging. Feel free to reopen if still relevant.