Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Picard AddOrReplaceReadGroups Error

    Hello all,

    I am getting the following error when I try to run the AddOrReplaceReadGroups function on picard.


    net.sf.picard.sam.AddOrReplaceReadGroups INPUT=/storage/isu/reecy_lab/tmp_eric/9111.1.12.bwa.sorted.bam OUTPUT=/storage/isu/reecy_lab/tmp_eric/9111.1.12.bwa.sorted.corrected.bam SORT_ORDER=coordinate RGLB=BWA RGPL=illumina RGPU=run RGSM=9111 RGID=1 TMP_DIR=/tmp/ercfrtz VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
    INFO 2011-03-25 14:33:23 AddOrReplaceReadGroups Created read group ID=1 PL=illumina LB=BWA SM=9111

    [Fri Mar 25 14:36:18 CDT 2011] net.sf.picard.sam.AddOrReplaceReadGroups done.
    Runtime.totalMemory()=922746880
    Exception in thread "main" net.sf.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; streamed file (filename not available)
    at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:199)
    at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:189)
    at net.sf.samtools.util.BinaryCodec.writeString(BinaryCodec.java:296)
    at net.sf.samtools.util.BinaryCodec.writeString(BinaryCodec.java:283)
    at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:128)
    at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:37)
    at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:185)
    at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:140)
    at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:157)
    at net.sf.picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:93)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117)
    at net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:61)
    Caused by: java.io.IOException: No space left on device
    at java.io.FileOutputStream.writeBytes(Native Method)
    at java.io.FileOutputStream.write(Unknown Source)
    at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
    at java.io.BufferedOutputStream.write(Unknown Source)
    at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:197)
    ... 12 more


    Any suggestions?

  • #2
    Carefully read your stack trace:
    Originally posted by ercfrtz View Post
    [Fri Mar 25 14:36:18 CDT 2011] net.sf.picard.sam.AddOrReplaceReadGroups done.
    Runtime.totalMemory()=922746880
    Exception in thread "main" net.sf.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; streamed file (filename not available)
    at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:199)
    at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:189)
    at net.sf.samtools.util.BinaryCodec.writeString(BinaryCodec.java:296)
    at net.sf.samtools.util.BinaryCodec.writeString(BinaryCodec.java:283)
    at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:128)
    at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:37)
    at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:185)
    at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:140)
    at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:157)
    at net.sf.picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:93)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
    at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117)
    at net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:61)
    Caused by: java.io.IOException: No space left on device
    at java.io.FileOutputStream.writeBytes(Native Method)
    at java.io.FileOutputStream.write(Unknown Source)
    at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
    at java.io.BufferedOutputStream.write(Unknown Source)
    at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:197)
    ... 12 more
    If the problem isn't the dir you're writing in, use an alternative temp dir (in stead of the default /tmp) with sufficient space (check Picard manual).

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    51 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X