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10 votes

Running SnakeMake on cluster

You can omit --nodes, you need the following: ...
Devon Ryan's user avatar
  • 19.6k
4 votes

How can I specify an email address in the SLURM snakemake json configuration file?

As noted by the comments and the SLURM manual (not so much bioinformatics related?) You need the following terms in your batch/queuing command: ...
story's user avatar
  • 1,573
3 votes

How to perform bowtie2 analysis with slurm?

It seems you do not have bowtie installed or loaded. Use module load bowtie2 together when you load samtools.
Phoenix Mu's user avatar
2 votes

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

The issue was that I supplied wrong indexes during fastq files generation, however, they were generated successfully, and only the next step failed with not that ...
Nikita Vlasenko's user avatar
2 votes

Nextflow scheduler job doesn't end upon successful workflow completion

How do you know your workflow actually finishes successfully? One way to check the workflow termination status is to use the workflow.onComplete and ...
Steve's user avatar
  • 3,109
2 votes

How can I run the latest version of samtools on Slurm?

I would start with: module avail Then look to see (a) if there is a samtools module avilable and (b) exactly what it's called. If it's called samtools/1.11 then: <...
Liam McIntyre's user avatar
1 vote

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

Simple answer The answer is this should be done via due process. A 1 hour time limit is harsh on any system. I'd talk with your line manager to justify your CPU time and then put the case to the Slurm ...
M__'s user avatar
  • 12.6k

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