<p>You're not using wildcards the way snakemake is equipped to work with them. See:</p>
<ol>
<li>FAQs such as <a href="https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-run-my-rule-on-all-files-of-a-certain-directory" rel="nofollow noreferrer">https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-run-my-rule-on-all-files-of-a-certain-directory</a> and <a href="https://snakemake.readthedocs.io/en/stable/project_info/faq.html#i-don-t-want-expand-to-use-the-product-of-every-wildcard-what-can-i-do" rel="nofollow noreferrer">https://snakemake.readthedocs.io/en/stable/project_info/faq.html#i-don-t-want-expand-to-use-the-product-of-every-wildcard-what-can-i-do</a></li>
<li><a href="https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#wildcards" rel="nofollow noreferrer">https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#wildcards</a></li>
</ol>

CC BY-SA 4.0
2022-10-17T20:26:04.173Z
2022-10-17T20:26:04.173Z
Ram RS
<p>I'm trying to run a snakefile for the first time with limited coding experience using salmon to index a reference genome. I'm not too sure what I'm doing wrong based on this error message.</p>
<pre><code>Error: Building DAG of jobs...
MissingRuleException:
No rule to produce snakefile (if you use input functions make sure that they don't raise unexpected exceptions).
</code></pre>
<p>Code:</p>
<pre><code>rule salmon_index:
        input:
                R1=&quot;sequences/*R1.fastq.gz&quot;,
                R2=&quot;sequences/*R2.fastq.gz&quot;
        output:
                Index=&quot;results/salmon_index&quot;
        shell:
                &quot;&quot;&quot;
                salmon index --threads 8 -t references/genome.fa.gz -i salmon_index
                &quot;&quot;&quot;
</code></pre>

<rna-seq><python><snakemake><conda><salmon>
Snakemake MissingRuleException
# Snakemake MissingRuleException

(Asked by: username_0 on 2022-10-17)

I'm trying to run a snakefile for the first time with limited coding experience using salmon to index a reference genome. I'm not too sure what I'm doing wrong based on this error message.
Error: Building DAG of jobs...
MissingRuleException:
No rule to produce snakefile (if you use input functions make sure that they don't raise unexpected exceptions).

Code:
rule salmon_index:
        input:
                R1="sequences/*R1.fastq.gz",
                R2="sequences/*R2.fastq.gz"
        output:
                Index="results/salmon_index"
        shell:
                """
                salmon index --threads 8 -t references/genome.fa.gz -i salmon_index
                """

**Tags:** rna-seq, python, snakemake, conda, salmon

---

## 1 answers

### Answer by username_1 on 2022-10-17. Score: 2

You're not using wildcards the way snakemake is equipped to work with them. See:

1. FAQs such as <https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-run-my-rule-on-all-files-of-a-certain-directory> and <https://snakemake.readthedocs.io/en/stable/project_info/faq.html#i-don-t-want-expand-to-use-the-product-of-every-wildcard-what-can-i-do>
2. <https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#wildcards>


---

