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PouletAxel / SIP

SIP: Significant Interaction Peak caller
GNU General Public License v3.0
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java.lang.NumberFormatException #24

Open Jiangyuan-Liu opened 3 days ago

Jiangyuan-Liu commented 3 days ago

Hi,

I got the following error messages when I ran "java -jar SIP-1.6.4.jar cool". Thanks.

Exception in thread "main" java.lang.NumberFormatException: For input string: "(/home/jiangyuan"
        at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67)
        at java.base/java.lang.Integer.parseInt(Integer.java:588)
        at java.base/java.lang.Integer.parseInt(Integer.java:685)
        at plop.sipMain.Hic_main.testTools(Hic_main.java:532)
        at plop.sipMain.Hic_main.main(Hic_main.java:287)

I created a conda env as shown below:

conda create -n SIP cooler=0.8.6 cooltools=0.3.2
conda activate SIP
conda install -c conda-forge openjdk
> java -version
openjdk version "22.0.1-internal" 2024-04-16
OpenJDK Runtime Environment (build 22.0.1-internal-adhoc.conda.src)
OpenJDK 64-Bit Server VM (build 22.0.1-internal-adhoc.conda.src, mixed mode, sharing)

It works for "java -jar SIP-1.6.4.jar -h"

#SIP Version 1 run with java 8

Usage:
        hic <hicFile> <chrSizeFile> <Output> <juicerToolsPath> [options]
        cool <mcoolFile> <chrSizeFile> <Output> <cooltoolsPath> <coolerPath> [options]
        processed <Directory with processed data> <chrSizeFile> <Output> [options]

Parameters:
         chrSizeFile: path to the chr size file, with the same name of the chr as in the hic file (i.e. chr1 does not match Chr1 or 1)
        -res: resolution in bp (default 5000 bp)
PouletAxel commented 2 days ago

Hi, Thanks, i will try to find the solution as soon as possible. Best Axel