Questions tagged [slurm]

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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 ...
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  • 1,224
0 votes
0 answers
119 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 ...
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  • 165
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1 answer
59 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 ...
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0 votes
1 answer
124 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 ...
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1 vote
1 answer
222 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: ...
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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 ...
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0 votes
1 answer
2k views

10X cellranger count, [error] The chemistry was unable to be automatically determined

While running cellranger count using the following .slurm file: ...
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