<p>I am trying to run a script that assess the quality of a transcriptomic assembly, a de novo assembly using a tool called Transrate. To install the tool I followed the prompts in <a href="https://bioconda.github.io/recipes/transrate/README.html" rel="nofollow noreferrer">https://bioconda.github.io/recipes/transrate/README.html</a>  I work on an HPC therefore I used <code>module load mamba/23.3.1-0</code> created a mamba environment and called it <code>transrate</code>, I installed the tool using <code>mamba install transrate</code> and then I activated the environment called <code>transrate</code> using  <code>mamba activate transrate</code>. When I use <code>mamba list</code> it shows me its dependencies and when I use <code>gem list</code> I can see that transrate has been installed. On my bash script this is what I have:</p>
<pre><code>module load mamba/23.3.1-0
# Activate the Conda environment
mamba activate transrate
echo &quot;Assembly assessment with Transrate&quot;
transrate --assembly /path/to/my/assembly/Trinity.fasta --left trimmed_SRR609893_1.fastq.gz --right trimmed_SRR609893_2.fastq.gz --threads 8 --output /path/to/my/output/directory/
echo &quot;Assement complete&quot; 
</code></pre>
<p>When I submit this job in a bash script using <code>sbatch transrate.sh</code> on my cluster I get an error log file which shows me this:</p>
<pre><code>Run 'mamba init' to be able to run mamba activate/deactivate
and start a new shell session. Or use conda to activate/deactivate.

/var/lib/slurm/slurmd/job9637707/slurm_script: line 15: transrate: command not found
</code></pre>
<p>I don't know what the issue is because when I use the <code>mamba init</code> it says no changes done, and I am still able to use mamba activate or deactivate. I do not understand why it says command <code>transrate</code> is not found yet on that environment it is present when using &quot;gem list&quot;.</p>
<p>May I please get assistance on the matter, ,or get an alternative that I can use to assess a de novo assembly.</p>

CC BY-SA 4.0
2024-05-28T06:28:31.077Z
Two things: try adding `mamba init` above `mamba activate transrate`, and you may need to install a 'patched' transrate from a different source, e.g. the Oyster River Protocol version (https://github.com/macmanes-lab/Oyster_River_Protocol/blob/master/software/orp-transrate.tar.gz)
jared_mamrot
CC BY-SA 4.0
2024-06-04T13:57:58.787Z
Can you also check if the slurm job has access to the transrate binary? (i.e., take the path from `which transrate` from your home environment and check if that file is available in the job environment). Sometimes you might need to set the `PATH` variable depending on how the slurm jobs set up their environment.
dthorbur
<rna-seq><assembly><transcriptome><bioconda><hpc>
Assessing the quality of an assembly
# Assessing the quality of an assembly

(Asked by: username_0 on 2024-05-27)

I am trying to run a script that assess the quality of a transcriptomic assembly, a de novo assembly using a tool called Transrate. To install the tool I followed the prompts in https://bioconda.github.io/recipes/transrate/README.html  I work on an HPC therefore I used module load mamba/23.3.1-0 created a mamba environment and called it transrate, I installed the tool using mamba install transrate and then I activated the environment called transrate using  mamba activate transrate. When I use mamba list it shows me its dependencies and when I use gem list I can see that transrate has been installed. On my bash script this is what I have:
module load mamba/23.3.1-0
# Activate the Conda environment
mamba activate transrate
echo "Assembly assessment with Transrate"
transrate --assembly /path/to/my/assembly/Trinity.fasta --left trimmed_SRR609893_1.fastq.gz --right trimmed_SRR609893_2.fastq.gz --threads 8 --output /path/to/my/output/directory/
echo "Assement complete" 

When I submit this job in a bash script using sbatch transrate.sh on my cluster I get an error log file which shows me this:
Run 'mamba init' to be able to run mamba activate/deactivate
and start a new shell session. Or use conda to activate/deactivate.

/var/lib/slurm/slurmd/job9637707/slurm_script: line 15: transrate: command not found

I don't know what the issue is because when I use the mamba init it says no changes done, and I am still able to use mamba activate or deactivate. I do not understand why it says command transrate is not found yet on that environment it is present when using "gem list".
May I please get assistance on the matter, ,or get an alternative that I can use to assess a de novo assembly.

**Tags:** rna-seq, assembly, transcriptome, bioconda, hpc
> **Comments:**
> **username_1**: Two things: try adding `mamba init` above `mamba activate transrate`, and you may need to install a 'patched' transrate from a different source, e.g. the Oyster River Protocol version (https://github.com/macmanes-lab/Oyster_River_Protocol/blob/master/software/orp-transrate.tar.gz)  
> **username_2**: Can you also check if the slurm job has access to the transrate binary? (i.e., take the path from `which transrate` from your home environment and check if that file is available in the job environment). Sometimes you might need to set the `PATH` variable depending on how the slurm jobs set up their environment.  

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## 0 answers

