Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-28T06:28:31.077Z
Comments.Text: 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)
Comments.UserDisplayName: jared_mamrot
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-06-04T13:57:58.787Z
Comments.Text: 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.
Comments.UserDisplayName: dthorbur
Tags: <rna-seq><assembly><transcriptome><bioconda><hpc>
Title: Assessing the quality of an assembly
ThreadText: # 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.  
  
  ---
  
  ## 0 answers
  
  