Questions tagged [slurm]
The slurm tag has no usage guidance.
8
questions
1
vote
1
answer
95
views
bcbio run not running samples in parallel
Sorry for the cross post but I'm not getting a response on bcbio github:
I'm trying to run bcbio on 20 samples and it's only running one at a time as it steps through the yaml seemingly. I'm using ...
- 11
3
votes
1
answer
642
views
Nextflow scheduler job doesn't end upon successful workflow completion
Bug fixed
This issue appears to have been fixed in latest Nextflow: https://github.com/nextflow-io/nextflow/issues/2693
I've been using ...
- 1,354
1
vote
0
answers
250
views
SLURM script for running RSEM star fails
If you have worked on cluster with submitting jobs, please help me in resolving the following error.
I am running rsem pipeline to generate star index. In principal STAR requires more than 30G of RAM ...
- 237
0
votes
1
answer
223
views
How can I run the latest version of samtools on Slurm?
I am trying to run the following script on slurm to extract information from .sam files. While everything is perfect on my local machine with the samtools version 1.11, it does not work on slurm. I ...
0
votes
1
answer
323
views
How to perform bowtie2 analysis with slurm?
I am trying to run my alignment script that works locally, using SBATCH.
Official manual for bowtie2 says I can use ...
1
vote
1
answer
474
views
How can I specify an email address in the SLURM snakemake json configuration file?
I am working on a SLURM-based cluster. I am currently using the following slurm json file:
...
- 2,459
8
votes
2
answers
4k
views
Running SnakeMake on cluster
I do not understand how to specify correctly the parameters on a SLURM cluster for snakemake to use them. I tried submitting the ...
- 2,558
1
vote
1
answer
3k
views
10X cellranger count, [error] The chemistry was unable to be automatically determined
While running cellranger count using the following .slurm file:
...
- 2,558