Hi all,
I am having some issues with picards FixMateInformation functions and was wondering if anyone has had similar problems. I have bam files which have been had duplicates marked using picard and local realignment around indels with GATK, but when I then follow with FixMateInformation it runs nicely for a while before I get the following error
Exception in thread "main" net.sf.samtools.util.RuntimeIOException: java.io.IOException: No space left on device
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:228)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:150)
at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:157)
at net.sf.picard.sam.FixMateInformation.writeAlignment(FixMateInformation.java:259)
at net.sf.picard.sam.FixMateInformation.doWork(FixMateInformation.java:181)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118)
at net.sf.picard.sam.FixMateInformation.main(FixMateInformation.java:74)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.write(Native Method)
at org.xerial.snappy.SnappyOutputStream.writeInt(SnappyOutputStream.java:105)
at org.xerial.snappy.SnappyOutputStream.dump(SnappyOutputStream.java:126)
at org.xerial.snappy.SnappyOutputStream.flush(SnappyOutputStream.java:100)
at org.xerial.snappy.SnappyOutputStream.close(SnappyOutputStream.java:137)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:219)
... 7 more
No new fixed files result from this apart from empty temp files. I tried using samtools fix mate, and I thought it worked until I opened the new bams with IGV and noticed my reads were in red because the pairs are not mapped!
Any help with this would be much appreciated.
Many thanks,
Elliott
I am having some issues with picards FixMateInformation functions and was wondering if anyone has had similar problems. I have bam files which have been had duplicates marked using picard and local realignment around indels with GATK, but when I then follow with FixMateInformation it runs nicely for a while before I get the following error
Exception in thread "main" net.sf.samtools.util.RuntimeIOException: java.io.IOException: No space left on device
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:228)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:150)
at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:157)
at net.sf.picard.sam.FixMateInformation.writeAlignment(FixMateInformation.java:259)
at net.sf.picard.sam.FixMateInformation.doWork(FixMateInformation.java:181)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118)
at net.sf.picard.sam.FixMateInformation.main(FixMateInformation.java:74)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.write(Native Method)
at org.xerial.snappy.SnappyOutputStream.writeInt(SnappyOutputStream.java:105)
at org.xerial.snappy.SnappyOutputStream.dump(SnappyOutputStream.java:126)
at org.xerial.snappy.SnappyOutputStream.flush(SnappyOutputStream.java:100)
at org.xerial.snappy.SnappyOutputStream.close(SnappyOutputStream.java:137)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:219)
... 7 more
No new fixed files result from this apart from empty temp files. I tried using samtools fix mate, and I thought it worked until I opened the new bams with IGV and noticed my reads were in red because the pairs are not mapped!
Any help with this would be much appreciated.
Many thanks,
Elliott
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