two issues when I ran juicer with a public HiC data.

[Wei Wu]

Hi,

I use juicer-1.5.6 to run a HiC data and it reported several error messages. I'am wonder what's the reason and how I could do for fix this. 

1. The first error message is :

$more dup-rm.err 

rm: cannot remove ‘aligned/*_msplit*_optdups.txt’: No such file or directory

I found an answer here: https://groups.google.com/forum/#!searchin/3d-genomics/msplit*_optdups.txt$3A$20No$20such$20file$20or$20directory%7Csort:date/3d-genomics/DCyyfHsGx94/NH0CbJ6cAQAJ

"The opt dups error just means no optical duplicates were found, which might happen depending on your sequencer (optical dups just looks at read name). It's not a big deal - it just means the library complexity estimate will be off and all the duplicates will be in the dups.txt file. "

Does it mean I can just ignore it and it will not affect the results?

2. the second one is:

$more hic-5616298.err

java.lang.NumberFormatException: For input string: "chr2"

            at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

            at java.lang.Integer.parseInt(Integer.java:580)

            at java.lang.Integer.parseInt(Integer.java:615)

            at juicebox.tools.utils.original.AsciiPairIterator.advance(AsciiPairIterator.java:224)

            at juicebox.tools.utils.original.AsciiPairIterator.next(AsciiPairIterator.java:270)

            at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:505)

            at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:383)

            at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:293)

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

            at juicebox.tools.HiCTools.main(HiCTools.java:96)

 

$more hic30-5616299.err 

java.lang.NumberFormatException: For input string: "chr2"

            at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)

            at java.lang.Integer.parseInt(Integer.java:580)

            at java.lang.Integer.parseInt(Integer.java:615)

            at juicebox.tools.utils.original.AsciiPairIterator.advance(AsciiPairIterator.java:224)

            at juicebox.tools.utils.original.AsciiPairIterator.next(AsciiPairIterator.java:270)

            at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:505)

            at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:383)

            at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:293)

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

            at juicebox.tools.HiCTools.main(HiCTools.java:96)

I have no idea about this, does anybody help me?

Thanks!

Best,

Wei