error in txt to hic

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liuzhe...@gmail.com

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Oct 24, 2018, 9:38:59 PM10/24/18
to 3D Genomics
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

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Oct 24, 2018, 10:11:17 PM10/24/18
to 3D Genomics
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

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Oct 25, 2018, 9:22:01 AM10/25/18
to liuzhe...@gmail.com, 3D Genomics
You need to pass in the memory flags -xmx with at least 8g. 

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Neva Cherniavsky Durand, Ph.D.
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