GATK4 MarkDuplicates的htsjdk.samtools.SAMException: /tmp/.tmpnot found& (Too many open files)报错解决

GATK4 MarkDuplicates的htsjdk.samtools.SAMException: /tmp/.tmpnot found& (Too many open files)报错解决

本小白在服务器之前运行GATK4 MarkDuplicates完全没有问题，忽然有一天同样的文件同样的代码发现无法运行，并且报错如下，经过七七四十九天的研究，头都炸了终于发现了解决办法。

发现只要在跑GATK4 MarkDuplicates 加上参数–MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 3000 （默认的是8000，改为3000，如果还不行的话改的更小直到能跑）即可解决。

To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

htsjdk.samtools.SAMException: /tmp/anjie/CSPI.tmp5012020104068677848/3581.tmpnot found

at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(FileAppendStreamLRUCache.java:64)

at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(FileAppendStreamLRUCache.java:49)

at htsjdk.samtools.util.ResourceLimitedMap.get(ResourceLimitedMap.java:76)

at htsjdk.samtools.CoordinateSortedPairInfoMap.getOutputStreamForSequence(CoordinateSortedPairInfoMap.java:180)

at htsjdk.samtools.CoordinateSortedPairInfoMap.put(CoordinateSortedPairInfoMap.java:164)

at picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap.put(DiskBasedReadEndsForMarkDuplicatesMap.java:65)

at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:578)

at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:270)

at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:309)

at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)

at org.broadinstitute.hellbender.Main.main(Main.java:289)

Caused by: java.io.FileNotFoundException: /tmp/anjie/CSPI.tmp5012020104068677848/3581.tmp (Too many open files)

at java.base/java.io.FileOutputStream.open0(Native Method)

at java.base/java.io.FileOutputStream.open(FileOutputStream.java:298)

at java.base/java.io.FileOutputStream.(FileOutputStream.java:237)

at htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.makeValue(FileAppendStreamLRUCache.java:61)

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