error in txt to hic

[liuzhe...@gmail.com]

Dear all,

Thanks for involving this discussion. When I run these scripts:

awk '{if ($3 > $7){ print $1, $6, $7, $8, $9, $11, $2, $3, $4, $5, $10}else {print}}' merged_nodups.txt > merged_nodups1.txt

sort -k3,3d -k7,7d merged_nodups1.txt > merged_nodups2.txt

java  -Xms16000m -Xmx16000m -jar /home/liuzhe/Software/juicer/juicer_tools.jar pre merged_nodups2.txt merged_nohup.hic hg19

 (Note that: nodups.txt file is fine)

There are some errors occured:

Not including fragment map

Start preprocess

Writing header

Writing body

Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded

        at java.lang.String.substring(String.java:1969)

        at java.lang.String.subSequence(String.java:2003)

        at com.google.common.base.Splitter$SplittingIterator.computeNext(Splitter.java:612)

        at com.google.common.base.Splitter$SplittingIterator.computeNext(Splitter.java:522)

        at com.google.common.base.AbstractIterator.tryToComputeNext(AbstractIterator.java:64)

        at com.google.common.base.AbstractIterator.hasNext(AbstractIterator.java:59)

        at com.google.common.base.Splitter.splitToList(Splitter.java:421)

        at juicebox.tools.utils.original.AsciiPairIterator.advance(AsciiPairIterator.java:106)

        at juicebox.tools.utils.original.AsciiPairIterator.next(AsciiPairIterator.java:247)

        at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:498)

        at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:376)

        at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:286)

        at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:105)

        at juicebox.tools.HiCTools.main(HiCTools.java:98)

Could anyone can figure it out?

Looking forward to your answer?

Best wishes,

Zhe

[liuzhe...@gmail.com]

It should be:

sort -k2,2d -k7,7d merged_nodups1.txt > merged_nodups2.txt

在 2018年10月25日星期四 UTC+8上午9:38:59，liuzhe...@gmail.com写道：

[Neva Durand]

You need to pass in the memory flags -xmx with at least 8g. 

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org