Failure in creating .hic file by pre command: java.lang.NumberFormatException: For input string: "chr1" #238
Comments
|
It doesn’t look like your file is in one of these formats:
https://github.com/aidenlab/juicer/wiki/Pre#file-format
On Sat, Aug 28, 2021 at 9:50 AM yuanyuanhe2021 ***@***.***> wrote:
Hi, I was trying to create a .hic file from my sorted file
*48072_allValidPairs.pre_juicebox_sorted* by the following command:
java -jar ../apps/juicer_tools_1.11.04_jcuda.0.8.jar pre
tmp/48072_allValidPairs.pre_juicebox_sorted ./test_by_juicepre.hic hg19
but it give me the error:
WARN [2021-08-28T15:23:31,190] [Globals.java:138] [main] Development mode
is enabled
Not including fragment map
Start preprocess
Writing header
Writing body
java.lang.NumberFormatException: For input string: "chr1"
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:216)
at
juicebox.tools.utils.original.AsciiPairIterator.next(AsciiPairIterator.java:271)
at
juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:555)
at
juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:653)
at
juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:413)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:122)
at juicebox.tools.HiCTools.main(HiCTools.java:96)
My input file is organized in th format
and the first several lines are like this:
HWI-D00645:88:C7HBDANXX:6:1111:2926:93160 0 chr1 13364 0 1 chr1 12636433 1
HWI-D00645:88:C7HBDANXX:6:2103:11886:76007 1 chr1 13465 0 0 chr1 1386430 1
HWI-D00645:88:C7HBDANXX:6:2215:2638:47725 0 chr1 13864 0 1 chr1 11330574 1
HWI-D00645:88:C7HBDANXX:6:2106:14571:65098 1 chr1 13877 0 1 chr11 293293 1
HWI-D00645:88:C7HBDANXX:6:2211:3904:49818 1 chr1 13052 0 1 chr11 627695 1
HWI-D00645:88:C7HBDANXX:6:1102:17272:98283 1 chr1 13039 0 0 chr12 1405896 1
HWI-D00645:88:C7HBDANXX:6:1103:16267:71707 0 chr1 13469 0 0 chr12 207718 1
HWI-D00645:88:C7HBDANXX:6:1313:15280:85241 1 chr1 13503 0 1 chr12 283318 1
I thought it might be the problem of the chromosome name in my inputfile
is wrote in strings like "chr1" "chr2" but not in numeric format like "1"
"2". But others who put their cases online can run it well with chromosome
named as "chr1""chr2".
Could you please tell me how to solve it?
Thank you very much!
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Assistant Professor | Molecular and Human Genetics
Aiden Lab | Baylor College of Medicine
www.aidenlab.org
|
Thank you so much. It's settled. |
Hi, I was trying to create a .hic file from my sorted file 48072_allValidPairs.pre_juicebox_sorted by the following command:
java -jar ../apps/juicer_tools_1.11.04_jcuda.0.8.jar pre tmp/48072_allValidPairs.pre_juicebox_sorted ./test_by_juicepre.hic hg19
but it give me the error:
WARN [2021-08-28T15:23:31,190] [Globals.java:138] [main] Development mode is enabled
Not including fragment map
Start preprocess
Writing header
Writing body
java.lang.NumberFormatException: For input string: "chr1"
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:216)
at juicebox.tools.utils.original.AsciiPairIterator.next(AsciiPairIterator.java:271)
at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:555)
at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:653)
at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:413)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:122)
at juicebox.tools.HiCTools.main(HiCTools.java:96)
My input file is organized in th format
and the first several lines are like this:
HWI-D00645:88:C7HBDANXX:6:1111:2926:93160 0 chr1 13364 0 1 chr1 12636433 1
HWI-D00645:88:C7HBDANXX:6:2103:11886:76007 1 chr1 13465 0 0 chr1 1386430 1
HWI-D00645:88:C7HBDANXX:6:2215:2638:47725 0 chr1 13864 0 1 chr1 11330574 1
HWI-D00645:88:C7HBDANXX:6:2106:14571:65098 1 chr1 13877 0 1 chr11 293293 1
HWI-D00645:88:C7HBDANXX:6:2211:3904:49818 1 chr1 13052 0 1 chr11 627695 1
HWI-D00645:88:C7HBDANXX:6:1102:17272:98283 1 chr1 13039 0 0 chr12 1405896 1
HWI-D00645:88:C7HBDANXX:6:1103:16267:71707 0 chr1 13469 0 0 chr12 207718 1
HWI-D00645:88:C7HBDANXX:6:1313:15280:85241 1 chr1 13503 0 1 chr12 283318 1
I thought it might be the problem of the chromosome name in my inputfile is wrote in strings like "chr1" "chr2" but not in numeric format like "1" "2". But others who put their cases online can run it well with chromosome named as "chr1""chr2".
Could you please tell me how to solve it?
Thank you very much!
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