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mkirsche / Jasmine

Jasmine: SV Merging Across Samples
MIT License
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Exception in thread "Thread-6" java.lang.OutOfMemoryError: Java heap space #42

Open jigaoxiang opened 2 years ago

jigaoxiang commented 2 years ago

Dear Dr， When I merge the 25 SV files，there is some errors about my memory？My commad line as below: jasmine file_list=merge1.txt out_file=merge.n.vcf out_dir=./ threads=6 And the error information as show follow:

Exception in thread "Thread-6" java.lang.OutOfMemoryError: Java heap space
        at java.base/java.util.Arrays.copyOf(Arrays.java:3689)
        at java.base/java.util.PriorityQueue.grow(PriorityQueue.java:305)
        at java.base/java.util.PriorityQueue.offer(PriorityQueue.java:344)
        at java.base/java.util.PriorityQueue.add(PriorityQueue.java:326)
        at KDTree.search(KDTree.java:244)
        at KDTree.kNearestNeighbor(KDTree.java:197)
        at VariantMerger.runMerging(VariantMerger.java:205)
        at ParallelMerger$MyThread.run(ParallelMerger.java:89)

Can you give some advice to deal with this? Thank your time! Best wishes

Ji gaoxiang

mas-agis commented 1 month ago

Hi, I run into the same problem. Did you find the way to figure it out? Best, Maulana