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3 votes
1 answer
104 views

How can I override the time limit set by my administrator on SLURM using snakemake?

I am running PGS Calculator on a High-Performance Computer with the operating system GNU/Linux. I have an executable script named pgs_hack.slurm containing the following code: ...
Cristian Riccio's user avatar
1 vote
1 answer
96 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 ...
t_creasman's user avatar
3 votes
1 answer
659 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 ...
Mark Ebbert's user avatar
  • 1,354
1 vote
0 answers
252 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 ...
Angelo's user avatar
  • 237
0 votes
1 answer
233 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 ...
Dmitrii Trubetskoy's user avatar
0 votes
1 answer
330 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 ...
Dmitrii Trubetskoy's user avatar
1 vote
1 answer
492 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: ...
Biomagician's user avatar
  • 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 ...
Nikita Vlasenko's user avatar
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: ...
Nikita Vlasenko's user avatar