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Old 05-10-2021, 08:11 AM   #1
gastonviarengo
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Location: Argentina

Join Date: Mar 2020
Posts: 3
Default bbduk memory error

Hello everyone,

I've installed bbmap throw 'sudo apt-get install bbmap' and also by downloading the package, untaring it and adding the path to the directory in the .bashrc file. However, when running "bbduk.sh --version" or a script "bbduk.sh -Xmx ..." I get the following error:

/usr/bin/bbduk.sh: línea 344: /usr/share/bbmap/calcmem: No existe el archivo o el directorio
/usr/bin/bbduk.sh: línea 345: setEnvironment: orden no encontrada
/usr/bin/bbduk.sh: línea 346: parseXmx: orden no encontrada
/usr/bin/bbduk.sh: línea 350: freeRam: orden no encontrada
java -Xmxm -Xmsm -cp /usr/share/java/bbmap.jar jgi.BBDuk --version
Invalid maximum heap size: -Xmxm
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

I've tried -Xmx with different amounts of memory and receive the same error. Also, the folder /calcmem does indeed do not exist. Any ideas on how to solve this problem?

Thank you!
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Old 05-10-2021, 10:38 AM   #2
GenoMax
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Location: East Coast USA

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Default

Cross-posted and answered here: https://www.biostars.org/p/9469494/#9469500

Please use that answer.
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