Got error message when run Juicer on Slurm - define the partition

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Jian-Qing Lin

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Jul 4, 2020, 1:15:51 PM7/4/20
to 3D Genomics
Hello,

I am a Postdoc in the Unversity of Copenhagen.

I am try to run Juicer on our HPC with Slurm.

However, once the Juicer began, I got an error message as below:

sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
/groups/hologenomics/software/Juicer/v1.5.6/SLURM/scripts/juicer.sh: line 520: [: ==: unary operator expected
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: long
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: long
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: long
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: long
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: long
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified
sbatch: error: invalid partition specified: commons
sbatch: error: Batch job submission failed: Invalid partition name specified


I have try to modified my slurm job script to define the partition. But we don't have  "short", "normal" or "long"  partition on our cluster, we only have hologenomics-long, hologenomics-short and hologenomics.
Do you know how to fix it?

Thanks.

Best
Jian-Qing

Neva Durand

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Jul 4, 2020, 9:28:42 PM7/4/20
to Jian-Qing Lin, 3D Genomics
You can send in the queue or partition with the "-q" flag.

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Jianqing Lin

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Jul 5, 2020, 5:32:17 AM7/5/20
to ne...@broadinstitute.org, 3d-ge...@googlegroups.com
It works now.
Thanks Neva!

Jian-Qing

————————

林剑青 Jian-Qing Lin

E-mail: linjian...@gmail.com; linji...@zju.edu.cn

Tel：+ 86 15705813889 (China); +45 71319022 (Denmark)

On 7/5/2020 08:57，Jian-Qing Lin<linjian...@gmail.com> wrote：
Thanks Neva!

I have used "-p hologenomics-long" but it still failed.

Jian-Qing



Neva Durand <ne...@broadinstitute.org> 于 2020年7月5日周日 03:28写道：
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