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I needed to stop falcon because it was filling the memory. Here is my fc_run.cfg (for a genome of size ~150Mb and a computer with 500GB memory):
`[General]`
`job_type=local`
`# list of files of the …
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I understand how to install and run this program with docker but how can I install and run the software without using docker on a HPC cluster which uses singularity?
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We have a working solution locally as well as Slurm. Let's get it running on SGE as well.
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Hi,
We (@emilyburke, @andrewejaffe and me) can successfully run salmon using 1 core in the SGE-managed cluster we have access to. The problem is that for some reason we have to request a lot of mem…
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Hi,
the time limit for the batchtools [waitForJobs](https://mllg.github.io/batchtools/reference/waitForJobs) function is 604800 seconds. I haven't seen a way to tell Pulsar or the SpiecEasi pulsar br…
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Currently, C-PAC generates SGE job files that presuppose the existence of a parallel environment named 'cpac' on the cluster. Users might use a parallel environment with a different name, and we shou…
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I ran a small number of subjects (6) on an sge cluster config in bpipe, I also have concurrency requirements set in the local pipeline (uses threads).
The pipeline did not run the stage complaining:
…
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Hello,
I am trying running an assembly with MaSuRCa but am getting an error at the step: "Computing super reads from PE".
here's the output with the error:
[xxxx@vic xxxx]$ cd Assembly_tes…
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Just bumped into this.
in `slurm.py` and presumably `sge.py` etc. the base code seems to look in the `job.config` for parameters.
https://github.com/flywheel-io/hpc-client/blob/88f61e1aa49b3364…
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This happened when adding new nodes:
```
!!! ERROR - Error occured while running plugin 'starcluster.plugins.sge.SGEPlugin':
!!! ERROR - remote command 'source /etc/profile && cd /opt/sge6 &&
!!! ERR…