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CLC Genomics Workbench & Assembly Cell

Connect to maestro.pasteur.fr directly from your machine at the Lab or through the VPN. X-forwarding (graphical display) is not allowed by the ssh.pasteur.fr  gateway.

How to use CLC Genomics#

Please, first follow the procedure to allow graphical display from the nodes. If you don't, CLC Genomics will terminate with an error and this kind of message will appear on your terminal:

Code Block (bash)

srun: error: x11: unable to connect node maestro-1001
error: unable to open file /tmp/slurm-spank-x11.26239808.0
slurmstepd: error: x11: unable to read DISPLAY value
Logging to /pasteur/homes/<your login>/.clcbio/workbench/log/clc-workbench.log

Exception: java.lang.NoClassDefFoundError thrown from the UncaughtExceptionHandler in thread "main"
srun: error: maestro-1001: task 0: Exited with exit code 1

To use CLC Genomics WorkBench, you need to tell SLURM that you want to allocate a node only accessible with the dedicated partitions clcgwb.  Thus, you must pass -p clcgwb to srun as in:

Code Block (bash)

login@maestro-submit ~ $ module av clc
-------------------------------------- /opt/gensoft/modules --------------------------------------
clc-assembly-cell/5.1.0(default)  CLCGenomicsWorkbench/11.0.1  CLCGenomicsWorkbench/20.0.4(default)   
login@maestro-submit ~ $ module load CLCGenomicsWorkbench/20.0.4
login@maestro-submit ~ $ srun --x11 -p clcgwb clcgenomicswb20

Do not forget the --x11 option which is required to display the graphic interface. Only 1 node, that is to say 64 cores, are dedicated to that tool on Maestro.

How to use CLC Assembly Cell command-line tools#

To use CLC Assembly Cell tools, you need to indicate to SLURM that you want to allocate a node allowed to run these tools. For that, use partition clcbio as in

Code Block (bash)

login@maestro-submit ~ $ module av clc
-------------------------------------- /opt/gensoft/modules --------------------------------------
clc-assembly-cell/5.1.0(default)  CLCGenomicsWorkbench/11.0.1  CLCGenomicsWorkbench/20.0.4(default)  
login@maestro-submit ~ $ module load clc-assembly-cell
login@maestro-submit ~ $ srun -c 3 -p clcbio  clc_assembler --cpus 3  <other options and arguments>

Of course, you can call these commands in batch scripts or loops of sbatch commands. 3 nodes are dedicated to these tools. You can't request more than 64 cores per srun/salloc/sbatch command.

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