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remove meryl slurm job
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DininduSenanayake committed Jun 12, 2024
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Expand Up @@ -269,33 +269,6 @@ Now we can run Mercury!
meryl count k=30 memory=4 threads=2 hifi.fastq.gz output read-db.meryl
```

??? note "`--wrap` ???"

Previously, we used the `sbatch` command to submit a slurm script to the cluster and the slurm job handler. The `sbatch` command can actually take a lot of parameters like the ones we included in the beginning of our script, and one of those parameters is `--wrap` which kind of wraps whatever command you give it in a Slurm wrapper so that the cluster can schedule it as if it was a Slurm script.

Take note that running a process in this manner is not reproducible. Unless you have access to the `history` logs, other researchers are not able to know what parameters you have used. Therefore, it is advisable to write it out in a Slurm script as below:

!!! terminal "code"

```bash
#!/bin/bash -e
#SBATCH --account=nesi02659
#SBATCH --job-name=meryl
#SBATCH --time=00:15:00
#SBATCH --cpus-per-task=2
#SBATCH --mem=4G
#SBATCH --partition=milan

# Modules
module purge
module load Merqury/1.3-Miniconda3

# Run
meryl count k=30 memory=4 threads=2 \
hifi.fastq.gz \
output read-db.meryl
```

That shouldn't take too long to run. Now we have a Meryl DB for our HiFi reads. If we're curious about the distribution of our _k_-mers, we can use Meryl generate a histogram of the counts to show us how often a _k_-mer occurs only once in the reads, twice, etc.

??? question "How would you go about trying to do this with meryl?"
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