Answers.Body: <p>If a value for <code>MAXKMERLENGTH</code> was not set when compiling <code>velveth</code>, VelvetOptimizer just uses the default <code>$maxhash</code> value of 31<sup><a href="https://github.com/tseemann/VelvetOptimiser/blob/2.2.6/VelvetOptimiser.pl#L110-L112" rel="nofollow noreferrer">1</a></sup>. The hash lengths that you specify on the command line must be less than or equal to this value to run the tool successfully. The solution is to re-compile <code>velveth</code> with a larger <code>MAXKMERLENGTH</code>, for example:</p>
  <pre><code>make 'MAXKMERLENGTH=69'
  </code></pre>
  <p>Alternatively, re-install using the <a href="/questions/tagged/bioconda" class="post-tag" title="show questions tagged &#39;bioconda&#39;" aria-label="show questions tagged &#39;bioconda&#39;" rel="tag" aria-labelledby="bioconda-container">bioconda</a> package manager:</p>
  <pre><code>conda install -c bioconda perl-velvetoptimiser
  </code></pre>
  <p>This package includes <a href="https://anaconda.org/bioconda/velvet" rel="nofollow noreferrer">velvet</a>, which is built using a much higher maximum k-mer length and is usually sufficient for most purposes: <code>MAXKMERLENGTH=191</code><sup><a href="https://github.com/bioconda/bioconda-recipes/blob/master/recipes/velvet/build.sh" rel="nofollow noreferrer">2</a></sup>.</p>
  
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Answers.CreationDate: 2023-01-17T02:49:52.767Z
Answers.LastActivityDate: 2023-01-17T02:49:52.767Z
Answers.UserDisplayName: Steve
Body: <p>I'm trying to use Velvet Optimizer for a De Novo Assembly; I set my hash-lengths to be between 55 and 69</p>
  <pre><code>/projects/path/to/perlscripts/VelvetOptimiser-2.2.6/VelvetOptimiser.pl -s 55 -e 69 -f '-shortPaired -fastq.gz -separate trial2.trimmed.paired.R1.fastq.gz trial2.trimmed.paired.R2.fastq.gz' -f '-short -fastq.gz trial2.trimmed.unpaired.R1.fastq.gz' -f '-short -fastq.gz trial2.trimmed.unpaired.R2.fastq.gz' -x 2
  </code></pre>
  <p>When I check the output file, it returns me with</p>
  <pre><code>Starting to check input parameters.
      Start hash value too high.  New start hash value is 31.
      End hash value not in workable range.  New end hash value is 31
  </code></pre>
  <p>Any idea where I could be going wrong in my command?</p>
  
Tags: <assembly>
Title: Velvet Optimizer automatically changes to hash-length 31
ThreadText: # Velvet Optimizer automatically changes to hash-length 31
  
  (Asked by: username_0 on 2023-01-16)
  
  I'm trying to use Velvet Optimizer for a De Novo Assembly; I set my hash-lengths to be between 55 and 69
  
  ```
  /projects/path/to/perlscripts/VelvetOptimiser-2.2.6/VelvetOptimiser.pl -s 55 -e 69 -f '-shortPaired -fastq.gz -separate trial2.trimmed.paired.R1.fastq.gz trial2.trimmed.paired.R2.fastq.gz' -f '-short -fastq.gz trial2.trimmed.unpaired.R1.fastq.gz' -f '-short -fastq.gz trial2.trimmed.unpaired.R2.fastq.gz' -x 2
  
  ```
  
  When I check the output file, it returns me with
  
  ```
  Starting to check input parameters.
      Start hash value too high.  New start hash value is 31.
      End hash value not in workable range.  New end hash value is 31
  
  ```
  
  Any idea where I could be going wrong in my command?
  
  **Tags:** assembly
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-01-17. Score: 4 | Accepted answer
  
  If a value for `MAXKMERLENGTH` was not set when compiling `velveth`, VelvetOptimizer just uses the default `$maxhash` value of 31[1](https://github.com/tseemann/VelvetOptimiser/blob/2.2.6/VelvetOptimiser.pl#L110-L112). The hash lengths that you specify on the command line must be less than or equal to this value to run the tool successfully. The solution is to re-compile `velveth` with a larger `MAXKMERLENGTH`, for example:
  
  ```
  make 'MAXKMERLENGTH=69'
  
  ```
  
  Alternatively, re-install using the [bioconda](/questions/tagged/bioconda "show questions tagged 'bioconda'") package manager:
  
  ```
  conda install -c bioconda perl-velvetoptimiser
  
  ```
  
  This package includes [velvet](https://anaconda.org/bioconda/velvet), which is built using a much higher maximum k-mer length and is usually sufficient for most purposes: `MAXKMERLENGTH=191`[2](https://github.com/bioconda/bioconda-recipes/blob/master/recipes/velvet/build.sh).
  
  
  ---
  
  