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NumberFormatException #355

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yuchun2323 opened this issue Jul 22, 2024 · 0 comments
Open

NumberFormatException #355

yuchun2323 opened this issue Jul 22, 2024 · 0 comments

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@yuchun2323
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Hi,
Great tools! And can anyone help the issue :
I am trying to convert merged_nodups.txt file to .hic file use pre.
juicer.sh -S final -g hg38 -d file -p hg38.chrom.sizes -y hg38_Arima.txt -z hg38.fa -D juicer

Not including fragment map
Start preprocess
Writing header
Writing body
java.lang.NumberFormatException: For input string: "260�93"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:492)
at java.lang.Integer.parseInt(Integer.java:527)
at juicebox.tools.utils.original.AsciiPairIterator.advance(AsciiPairIterator.java:218)
at juicebox.tools.utils.original.AsciiPairIterator.next(AsciiPairIterator.java:271)
at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:488)
at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:580)
at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:346)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:116)
at juicebox.tools.HiCTools.main(HiCTools.java:96)

Part of my merged_nodups.txt was posted below:
0 chr1 10005 0 0 chr1 248945772 1260595 14 37M1I10M5I12M5I80M * 7 30M21I20M1D53M1I24M * A00126:242:HHGM5DSX3:3:2434:13503:16454 A00126:242:HHGM5DSX3:3:2434:13503:16454
16 chr1 10447 0 16 chr1 248945875 1260595 6 3S65M * 23 53M2D68M1I24M * A00126:242:HHGM5DSX3:3:1525:30698:25191 A00126:242:HHGM5DSX3:3:1525:30698:25191

Thanks,
kalo

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