Closed TobiasHohl closed 2 weeks ago
Hi Tobi,
I'll have a look if I can reproduce this. Just to understand, you've only modified the cluster command to exclude deep9?
Best wishes,
Katarzyna
Hi Katarzyna,
yes, when I start the pipeline with the following command it works:
DNA-mapping --DAG --trim --trimmerOptions "-a nexteraF=CTGTCTCTTATA -A nexteraR=CTGTCTCTTATA" --dedup --mapq 2 -j 20 -i ./fastq/ -o ./sp/ hg38
Only when using the cluster config yaml as stated above the pipeline gets stuck.
Thanks for looking into this!
Best Tobi
Hi Tobi,
thanks for submitting the issue. Indeed, I can reproduce it. I'll have a look what might be causing this.
Best,
Katarzyna
Hi Tobi,
as an update, I will attempt to circumvent this and other slurm-related issues in snakePipes by implementing native slurm support available in more recent snakemake versions. This is now pending, as I need the IT to solve an issue related to the slurm folder on the package partition.
Best,
Katarzyna
Obsolete since cluster yamls have been deprecated.
Using the following command, I tried running the DNA-mapping pipeline using a customized cluster config yaml to circumvent issues with one node on our server:
DNA-mapping --DAG --trim --trimmerOptions '-a nexteraF=CTGTCTCTTATA -A nexteraR=CTGTCTCTTATA' --dedup --mapq 2 -j 20 -i ./fastq/ -o ./mapping/ hg38 --clusterConfigFile custom-cluster-config.yaml
Apparently, the pipeline always got stuck at the execution of the first rules (origFASTQ1 and origFASTQ2), no matter what name I gave the custom config yaml and no matter what output folder I assigned. This was not the case when using the default cluster configuration. Also, when I start the pipeline with the default and interrupt after the origFASTQ folder and its contents are created, I can restart with the custom config and it finishes.
Custom cluster config:
Edit: formatting