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Hi and thank you for all your work with this pipeline!
I am having a bit of trouble analyzing my PacBio Kinnex full length 16s rRNA data. The data I received from the sequencing center were alre…
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### Describe the bug
un called with config file /mnt/odd/rs/v1/output/log/pipeline_APP0Base/107925100_1/cpac_pipeline_config_195db324_2024-09-11T03-18-11Z.yml
raise exception
File "/code/run.…
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Opening an issue to triage the segfault that seems to be happening in th SGE tests.
For some time the SGE tests have been failing. When you look at the logs of [a recent run](https://github.com/das…
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### Operating System
Windows 10
### Other Linux
_No response_
### Workflow Version
v24.04.2
### Workflow Execution
Command line (Cluster)
### Other workflow execution
_No response_
### EPI2M…
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Hello,
I am trying to run YAMP on a cluster of type SGE. It put these information in "process" part of the nextflow.config file :
executor = 'sge'
queue = 'batch,batchbm'
I get the followin…
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I'm tracking down a very obscure error, where about 30% of submitted jobs, go into the `Eqw` state.
The error is always the same,
```-bash-4.2$ qstat -j 668 | grep error
error reason 1:…
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dask without progress bar is working well on ips and local BCBL.
Needs to test:
how to change config.yaml so that -N will give cluster job a proper name.
how to change config yaml to let SGE …
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## Prework
* [x] Read and agree to the [Contributor Code of Conduct](https://github.com/wlandau/crew.cluster/blob/main/CODE_OF_CONDUCT.md) and [contributing guidelines](https://github.com/ropensci/…
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### 📜 Description
while testing the SGE on private clusters, we found some issues with AWS specific annotations that worker-operator is adding.
```
// Note: Special treatment for AWS EKS cluste…
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In SGE land, parallel execution environments ``-pe smp `` are assigned memory on a per-slot basis. Right now, as the memory requirements increase for a pydpiper executor, more memory is requested for …