Re: [Samtools-help] Specify query length in SAM format?

[Alec W. <al...@br...>]

Hi John,

The code is failing to map a file that it is creating into memory.  Is 
there any way you can increase the amount of virtual memory available to 
your process (e.g. via invoking ulimit)?  I don't mean increasing -Xmx 
value because memory mapping doesn't use Java heap.  In fact, large Xmx 
value makes this problem more likely to happen because MarkDuplicates 
determines the size of a SortingLongCollection by looking at the max 
java heap size.  So, counterintuitively, reducing -Xmx value will reduce 
the chance that this problem will occur.  I don't understand why having 
run MergeSam prior to MarkDuplicates should matter -- once that process 
has terminated you would think that its virtual memory would be released.

-Alec

On 3/29/11 12:27 PM, John Knepper wrote:
> Is anybody having the issue of Mark Duplicates failing after using 
> MergeSam?  I've been getting some error :
>
> [Mon Mar 28 15:16:43 CDT 2011] net.sf.picard.sam.MarkDuplicates done.
> Runtime.totalMemory()=62781718528
> Exception in thread "main" net.sf.samtools.util.RuntimeIOException: 
> java.io.IOException: Map failed
>         at 
> net.sf.samtools.util.SortingLongCollection.spillToDisk(SortingLongCollection.java:179)
>         at 
> net.sf.samtools.util.SortingLongCollection.add(SortingLongCollection.java:113)
>         at 
> net.sf.picard.sam.MarkDuplicates.addIndexAsDuplicate(MarkDuplicates.java:511)
>         at 
> net.sf.picard.sam.MarkDuplicates.markDuplicateFragments(MarkDuplicates.java:565)
>         at 
> net.sf.picard.sam.MarkDuplicates.generateDuplicateIndexes(MarkDuplicates.java:479)
>         at 
> net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:115)
>         at 
> net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
>         at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:97)
> :set nu!
>
> , But it only seems to be happening when I use MergeSam prior to 
> removing duplicates
>
>
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