Hi,
I'm having trouble understanding some of the params with Picard- well not really understanding but I'm getting this error here:
...
INFO 2010-10-26 22:45:32 MarkDuplicates Read 40000000 records. Tracking 2669417 as yet unmatched pairs. 69542 records in RAM. Last sequence index: 2
INFO 2010-10-26 22:45:47 MarkDuplicates Read 41000000 records. Tracking 2725267 as yet unmatched pairs. 47482 records in RAM. Last sequence index: 2
INFO 2010-10-26 22:46:15 MarkDuplicates Read 42000000 records. Tracking 2779116 as yet unmatched pairs. 25059 records in RAM. Last sequence index: 2
[Tue Oct 26 22:46:36 CDT 2010] net.sf.picard.sam.MarkDuplicates done.
Runtime.totalMemory()=778698752
Exception in thread "main" net.sf.picard.PicardException: Exception writing ReadEnds to file.
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:74)
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:32)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:185)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:140)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:305)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:260)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:65)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:123)
at java.io.DataOutputStream.flush(DataOutputStream.java:106)
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:71)
... 7 more
...
Has anyone ever gotten this writing read ends to file error?
I'm having trouble understanding some of the params with Picard- well not really understanding but I'm getting this error here:
...
INFO 2010-10-26 22:45:32 MarkDuplicates Read 40000000 records. Tracking 2669417 as yet unmatched pairs. 69542 records in RAM. Last sequence index: 2
INFO 2010-10-26 22:45:47 MarkDuplicates Read 41000000 records. Tracking 2725267 as yet unmatched pairs. 47482 records in RAM. Last sequence index: 2
INFO 2010-10-26 22:46:15 MarkDuplicates Read 42000000 records. Tracking 2779116 as yet unmatched pairs. 25059 records in RAM. Last sequence index: 2
[Tue Oct 26 22:46:36 CDT 2010] net.sf.picard.sam.MarkDuplicates done.
Runtime.totalMemory()=778698752
Exception in thread "main" net.sf.picard.PicardException: Exception writing ReadEnds to file.
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:74)
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:32)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:185)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:140)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:305)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:260)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:65)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:123)
at java.io.DataOutputStream.flush(DataOutputStream.java:106)
at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:71)
... 7 more
...
Has anyone ever gotten this writing read ends to file error?
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