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You can omit --nodes, you need the following: #!/bin/bash #SBATCH --ntasks-per-node=1 #SBATCH -c threads_from_snakemake #SBATCH -p some_partition Commands go here For slurm, you may want to modify my SlurmEasy script. We use that with snakemake all the time, usually of the form: snakemake -c "SlurmEasy -t {threads} -n {rule} --mem-per-cpu {cluster.memory}...


As noted by the comments and the SLURM manual (not so much bioinformatics related?) You need the following terms in your batch/queuing command: --mail-type=ALL I used "ALL" which will send you all reports. If you just want the finish message then you would use "END" and "FAIL" like such: --mail-type=END,FAIL Here are the ...


It seems you do not have bowtie installed or loaded. Use module load bowtie2 together when you load samtools.


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: module load samtools/1.11 Should work, if it doesn't speak to your sys admin.


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 informative error.

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