net.sf.picard.PicardException: Error creating temporary ReadEnds file

seqanswers.com | 3 months ago
  1. 0

    Picard error - SEQanswers

    seqanswers.com | 3 months ago
    net.sf.picard.PicardException: Error creating temporary ReadEnds file
  2. 0

    GitHub comment 92#55352834

    GitHub | 2 years ago | Brett-CCG
    net.sf.picard.PicardException: /scratch/share/data/Wheat_IWGSC_RNA-seq_alignments/INRA_PE_alignments/SAM_files/complete/Wheat_BAM_files/picardTemp/CSPI.8709064633600382632.tmp/5526.tmpnot found
  3. 0

    Acceptance tests fail on ecryptfs mount

    GitHub | 5 years ago | gbacon
    java.lang.RuntimeException: java.io.FileNotFoundException: FitNesseRoot/files/testProgress/FitNesse.SuiteAcceptanceTests.SuiteSlimTests.ScenarioLibraryTestSuite.ScenarioLibariesOrderTests.ScenarioLibraryOrderSuite.ScenarioLibraryOrderTestParent.ScenarioLibraryOrderIsCorrect (File name too long)
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  5. 0

    Permission Denied when exporting

    GitHub | 4 years ago | Mic92
    java.io.FileNotFoundException: entities.tar.gz (Permission denied)
  6. 0

    CloudBees Back-up Plugin failing

    Stack Overflow | 3 years ago | garnerh42
    java.io.FileNotFoundException: /mnt/jenkinsbackup/backup-Jenkins Backup-19.tar.gz (Permission denied)

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Root Cause Analysis

  1. java.io.FileNotFoundException

    /media/1B3B8E0F52CC3359/mRNAsnp/DREM.4603601404094682558.tmp/32279.read_ends (Too many open files)

    at java.io.FileOutputStream.open()
  2. Java RT
    FileOutputStream.<init>
    1. java.io.FileOutputStream.open(Native Method)
    2. java.io.FileOutputStream.<init>(FileOutputStream.java:209)
    3. java.io.FileOutputStream.<init>(FileOutputStream.java:160)
    3 frames
  3. picard
    MarkDuplicates.main
    1. net.sf.picard.sam.DiskReadEndsMap.getOutputStreamForSequence(DiskReadEndsMap.java:170)
    2. net.sf.picard.sam.DiskReadEndsMap.put(DiskReadEndsMap.java:147)
    3. net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:278)
    4. net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109)
    5. net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:160)
    6. net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93)
    6 frames