<p>From a quick look at the manual, it looks like you are supposed to use just the <code>wrapper</code>, not combine the <code>wrapper</code> with a <code>shell</code>. Can you show me an example of such combined usage?</p>
<p>The error seems to suggest that the wrapper already has a <code>shell</code> directive that you <code>shell</code> conflicts with.</p>

CC BY-SA 4.0
2021-11-11T21:06:54.270Z
Thank you! In Output, I also had to remove the "./[out path]/" before the output file name, I guess the "--outdir" in Shell is sufficient. I got the files but still received the error: "Job Missing files after 5 seconds:
well01_S001_L001_R1_001.fastqc.html
well01_S001_L001_R1_001.fastqc.zip
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Job id: 0 completed successfully, but some output files are missing. 0" and I also waited for 60s and got the same error.
Swietenia
CC BY-SA 4.0
2021-11-11T19:16:57.397Z
2021-11-11T19:16:57.397Z
Ram RS
<p>I am trying to check the quality of RNA-Seq data from Illumina using fastqc in snakemake in a conda environment. I get the error &quot;Multiple run or shell keywords in rule run_fastqc&quot;.</p>
<p>Snakefile:</p>
<pre><code>rule run_fastqc:
    input:
        &quot;/[RNA fastq file path]/well01_S001_L001_R1_001.fastq.gz&quot;
    output:
        &quot;./[out path]/well01_S001_L001_R1_001.fastqc.html&quot;,
        &quot;./[out path]/well01_S001_L001_R1_001.fastqc.zip&quot;
    wrapper:
        &quot;0.79.0/bio/fastqc&quot;
    shell:
        &quot;fastqc {input} --outdir=./[out path]/&quot;
</code></pre>
<p>I've also tried:</p>
<pre><code>...
    shell:
        &quot;fastqc {input} -o ./[out path]/&quot;
...
    shell:
        &quot;fastqc -o ./[out path]/ {input}&quot;
...
    shell:
        &quot;fastqc {input}&quot;
        &quot;fastqc -o ./[out path]/&quot;
...
    shell:
        &quot;fastqc {input} &gt; -o ./[out path]/&quot;
</code></pre>
<p>Code:</p>
<pre><code>snakemake --cores 1 well01_S001_L001_R1_001.fastqc.html well01_S001_L001_R1_001.fastqc.zip
</code></pre>
<p>Output:</p>
<pre><code>SyntaxError in line 9 of /[path to Snakefile]/Snakefile:
Multiple run or shell keywords in rule run_fastqc. (Snakefile, line 9)
</code></pre>
<p>When I run fastqc alone (not in snakemake), it works and I get the two output files. How can I get snakemake to work?</p>
<p>Thank you for your time and help!</p>

<rna-seq><python><snakemake><quality-control><fastqc>
Snakemake Fastqc: "Multiple run or shell keywords in rule run_fastqc."
# Snakemake Fastqc: "Multiple run or shell keywords in rule run_fastqc."

(Asked by: username_0 on 2021-11-11)

I am trying to check the quality of RNA-Seq data from Illumina using fastqc in snakemake in a conda environment. I get the error "Multiple run or shell keywords in rule run_fastqc".
Snakefile:
rule run_fastqc:
    input:
        "/[RNA fastq file path]/well01_S001_L001_R1_001.fastq.gz"
    output:
        "./[out path]/well01_S001_L001_R1_001.fastqc.html",
        "./[out path]/well01_S001_L001_R1_001.fastqc.zip"
    wrapper:
        "0.79.0/bio/fastqc"
    shell:
        "fastqc {input} --outdir=./[out path]/"

I've also tried:
...
    shell:
        "fastqc {input} -o ./[out path]/"
...
    shell:
        "fastqc -o ./[out path]/ {input}"
...
    shell:
        "fastqc {input}"
        "fastqc -o ./[out path]/"
...
    shell:
        "fastqc {input} > -o ./[out path]/"

Code:
snakemake --cores 1 well01_S001_L001_R1_001.fastqc.html well01_S001_L001_R1_001.fastqc.zip

Output:
SyntaxError in line 9 of /[path to Snakefile]/Snakefile:
Multiple run or shell keywords in rule run_fastqc. (Snakefile, line 9)

When I run fastqc alone (not in snakemake), it works and I get the two output files. How can I get snakemake to work?
Thank you for your time and help!

**Tags:** rna-seq, python, snakemake, quality-control, fastqc

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## 1 answers

### Answer by username_1 on 2021-11-11. Score: 1 | Accepted answer

From a quick look at the manual, it looks like you are supposed to use just the `wrapper`, not combine the `wrapper` with a `shell`. Can you show me an example of such combined usage?

The error seems to suggest that the wrapper already has a `shell` directive that you `shell` conflicts with.

> **Comments:**
> **username_0**: Thank you! In Output, I also had to remove the "./[out path]/" before the output file name, I guess the "--outdir" in Shell is sufficient. I got the files but still received the error: "Job Missing files after 5 seconds: well01_S001_L001_R1_001.fastqc.html well01_S001_L001_R1_001.fastqc.zip This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. Job id: 0 completed successfully, but some output files are missing. 0" and I also waited for 60s and got the same error.  

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