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issue with running Crispr_DART pipeline #4

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dasn588 opened this issue Apr 5, 2023 · 0 comments
Open

issue with running Crispr_DART pipeline #4

dasn588 opened this issue Apr 5, 2023 · 0 comments

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@dasn588
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dasn588 commented Apr 5, 2023

Hi,
I tried to install Crispr_DART tool and its related dependency programs. I also downloaded separately GATK-v3.8-0-ge9d806836 and extracted the zip folder after which i got only GenomeAnalysisTK.jar file inside the folder. Next, I gave path for java and gatk in settings.yaml file along with all input files location as well as output directory. Finally when I tried to execute the program. It did not output any result files in the output gatk subfolder created inside the parent output folder Crispr_DART. When I checked the log files generated for gatk step, it was showing following error.

ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/data/ngs/programs/crispr_DART/tool_gatk_3.8/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...

Please help me to resolve the issue and generate complete result files.

Thanks
Nihar

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