Hi, I have the problem when I use the FastqToSam to convert my fastqfiles to sam files, I use the latest picard version.
I use the command line below:
java -jar picard.jar FastqToSam F1=94210_CGTACTAG_S2_L001_R1_001.fastq F2=94210_CGTACTAG_S2_L001_R2_001.fastq O=fastq_to_bam.bam USE_SEQUENTIAL_FASTQS=true QUALITY_FORMAT=Illumina ALLOW_AND_IGNORE_EMPTY_LINES=true USE_JDK_DEFLATER=true USE_JDK_INFLATER=true SM=for_tool_testing
And it has the bug like these
[Fri Nov 24 19:10:16 EST 2017] picard.sam.FastqToSam done. Elapsed time: 19.69 minutes.
Runtime.totalMemory()=3359113216
Exception in thread "Thread-106" Exception in thread "Thread-140" Exception in thread "Thread-83" Exception in thread "Thread-22" Exception in thread "Thread-20" Exception in thread "Thread-100" Exception in thread "Thread-14" Exception in thread "Thread-107" Exception in thread "Thread-51" Exception in thread "Thread-35" Exception in thread "Thread-125" Exception in thread "Thread-50" Exception in thread "Thread-94" Exception in thread "Thread-135" Exception in thread "Thread-31" Exception in thread "Thread-129" Exception in thread "Thread-136" htsjdk.samtools.util.RuntimeIOException: java.nio.file.NoSuchFileException: /tmp/yingma/sortingcollection.6119188463332115860.tmp
at htsjdk.samtools.util.IOUtil$DeletePathThread.run(IOUtil.java:374)
Caused by: java.nio.file.NoSuchFileException: /tmp/yingma/sortingcollection.6119188463332115860.tmp
at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
at sun.nio.fs.UnixFileSystemProvider.implDelete(UnixFileSystemProvider.java:244)
at sun.nio.fs.AbstractFileSystemProvider.delete(AbstractFileSystemProvider.java:103)