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