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Old 10-23-2017, 04:52 AM   #1
Lukas Hellmann
Junior Member
 
Location: Germany

Join Date: Jul 2015
Posts: 3
Default Java problem when using BBmap

Hi guys,

I am working on a cluster that was changed to CentOS 7.3.1611 and SLURM scheduler recently. Since the change I cannot use any of the BBmap tools any longer, they all quit with a java error.

For example:
bbduk.sh -Xmx400m in=test.fq out=out.fq ftl=10

results in:
Error occurred during initialization of VM
Could not reserve enough space for 819200KB object heap
srun: error: a0150: task 0: Exited with exit code 1
srun: Terminating job step 3196181.0

I have Java 1.8.0_121 installed. Using the -Xms flag did not solve the problem either.

Any ideas how to tackle the problem?

Last edited by Lukas Hellmann; 10-23-2017 at 05:10 AM.
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