<p>I have snakemake script doing fastqc with a wrapper but it errors out saying</p>
<pre><code>Command 'set -euo pipefail;  /home/mi/ppp/miniconda3/envs/meta/bin/python3.9 /workflow/.snakemake/scripts/tmpsl695gpr.wrapper.py' returned non-zero exit status 1.
  File &quot;/workflow/rules/fastqc.smk&quot;, line 32, in __rule_fastq1
  File &quot;/home/mi/ppp/miniconda3/envs/meta/lib/python3.9/concurrent/futures/thread.py&quot;, line 58, in run
</code></pre>
<p>my rule looks like this</p>
<pre><code>rule fastq1:
    input: 
        &quot;../resources/samples/{sample}_1.fq.gz&quot;
    output:
        html = &quot;../results/html/{sample}_1.fq.html&quot;,
        zip = &quot;../results/zip/{sample}_1.fq.zip&quot;
    conda: 
        &quot;../envs/meta.yaml&quot;
    log: 
        &quot;../results/logs/fastq_raw/fastq_raw_{sample}.log&quot;
    threads: 
        2
    wrapper:
        &quot;v1.5.0/bio/fastqc&quot;
</code></pre>
<p>I have a feeling this used to work before and my partner says it works fine on his machine but I can't find the issue.</p>
<p>I'm also doing this on a clean conda/mamba install and env.</p>
<p>EDIT:
Snakemake version is 7.7.0
I &quot;solved&quot; this by installing fastqc with conda... I mean am I stupid? Is it a requirement for a wrapper to also have the package installed? I don't think this was mentioned on the Snakemake website</p>
<p>(Im not sure wht mr communuty bot is complaining about the problem is the error message and me not being able to run the code..)</p>
<p>Thanks for reading.</p>

CC BY-SA 4.0
2022-05-20T18:15:35.490Z
Please include Snakemake version in question body.
merv
CC BY-SA 4.0
2022-05-20T23:58:58.997Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2022-05-22T05:31:15.220Z
Note that `set -euo pipefail` is something Snakemake adds by default to your shell commands. The fact that it appears in the error message is usually not relevant. The error likely has to do with something else in the command that the wrapper calls.
bli
<snakemake><conda>
set -euo pipefail in Snakemake wrapper
# set -euo pipefail in Snakemake wrapper

(Asked by: username_0 on 2022-05-20)

I have snakemake script doing fastqc with a wrapper but it errors out saying
Command 'set -euo pipefail;  /home/mi/ppp/miniconda3/envs/meta/bin/python3.9 /workflow/.snakemake/scripts/tmpsl695gpr.wrapper.py' returned non-zero exit status 1.
  File "/workflow/rules/fastqc.smk", line 32, in __rule_fastq1
  File "/home/mi/ppp/miniconda3/envs/meta/lib/python3.9/concurrent/futures/thread.py", line 58, in run

my rule looks like this
rule fastq1:
    input: 
        "../resources/samples/{sample}_1.fq.gz"
    output:
        html = "../results/html/{sample}_1.fq.html",
        zip = "../results/zip/{sample}_1.fq.zip"
    conda: 
        "../envs/meta.yaml"
    log: 
        "../results/logs/fastq_raw/fastq_raw_{sample}.log"
    threads: 
        2
    wrapper:
        "v1.5.0/bio/fastqc"

I have a feeling this used to work before and my partner says it works fine on his machine but I can't find the issue.
I'm also doing this on a clean conda/mamba install and env.
EDIT:
Snakemake version is 7.7.0
I "solved" this by installing fastqc with conda... I mean am I stupid? Is it a requirement for a wrapper to also have the package installed? I don't think this was mentioned on the Snakemake website
(Im not sure wht mr communuty bot is complaining about the problem is the error message and me not being able to run the code..)
Thanks for reading.

**Tags:** snakemake, conda
> **Comments:**
> **username_1**: Please include Snakemake version in question body.  
> **username_2**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_3**: Note that `set -euo pipefail` is something Snakemake adds by default to your shell commands. The fact that it appears in the error message is usually not relevant. The error likely has to do with something else in the command that the wrapper calls.  

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## 0 answers

