Picard AddOrReplaceReadGroups Error

[ercfrtz]

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?

[Bruins]

Carefully read your stack trace:

[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).