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've tried with -Xmx5g, -Xmx4g, -Xmx1g, -Xmx800m, -Xmx100m and without setting -Xmx on a 8 gb RAM machine) 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.
Also, the folder /calcmem does indeed do not exist. Any ideas on how to solve this problem?
Thank you!
I've re-tried download from SourceForge, unpack and add to PATH in .
bashrc
file (export PATH="/media/Archivos/Programas/BBMap_38.90:$PATH"
) but still not working. The hackish solution hasn't work either. Also installing from conda gave the following error:Any ideas?
I'll try reporting this issue to Ubuntu but I guess that can take a while to solve.
Please use the formatting bar (especially the
![code_formatting](https://image.ibb.co/fg0nMx/code_formatting.png)
code
option) to present your post better. You can use backticks for inline code (`text` becomestext
), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.