Answers.Body: <p>The main issue I can see is the filenames, and should be easily solvable.</p>
  <p>Simply put, LongStitch is <em>very</em> particular about filenames. It expects the input draft to have the extension .fa, and the input reads to have any from a range of extensions (your .fastq is perfectly fine, though).</p>
  <p>The main issue is that LongStitch expects the extensions to be <em>missing</em> from the command. So if your draft is draft is called <code>consensus.fa</code> and your reads are  <code>combined.fastq</code>, then the command would include something like <code>draft=consensus reads=combined</code>, not <code>draft=consensus.fa reads=combined.fastq</code>.</p>
  <p>(unsure if it accepts input from different directories, or whether you'll need to move your input to the same directory as well)</p>
  <p>More generally, when having issues with a particular tool which is available via github, I would encourage you to have a look at the 'Issues' or 'Help' section. What I normally do is to delete the 'is:issue is:open' terms in the search bar, which allows me to search for my bug among older, potentially solved issues (e.g. <a href="https://github.com/bcgsc/LongStitch/issues/54" rel="nofollow noreferrer">https://github.com/bcgsc/LongStitch/issues/54</a>), and also generally to check that the software is still supported.</p>
  <p>Good luck!</p>
  <p>(*that said, M_'s suggestion of using mamba is generally a good one, and has helped me with another LongStitch bug)</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-21T10:38:25.160Z
Answers.LastActivityDate: 2023-12-21T10:38:25.160Z
Answers.UserDisplayName: Laura
Answers.Body: <p>Could you download it from <code>conda</code> and try again? Its here, <a href="https://docs.conda.io/en/main/miniconda.html" rel="nofollow noreferrer">https://docs.conda.io/en/main/miniconda.html</a></p>
  <p>Then,</p>
  <pre><code>conda create --name myenv
  conda activate myenv
  conda install -c bioconda longstitch
  longstitch ...
  </code></pre>
  <p>Conda avoids all the build stuff.</p>
  <hr />
  <p>Notes</p>
  <p>If you find that &quot;conda&quot; is slow and doesn't ever load.</p>
  <p>There is an alternative to conda called <strong>mamba</strong>, this is fast and designed to address this exact issue. I have never needed to use it so the following is a rough guide only.</p>
  <p>Download and install via</p>
  <pre><code>conda create --name myenv
  conda activate myenv
  conda install -c conda-forge mamba
  </code></pre>
  <p>The documentation is here, <a href="https://mamba.readthedocs.io/en/latest/user_guide/mamba.html" rel="nofollow noreferrer">https://mamba.readthedocs.io/en/latest/user_guide/mamba.html</a></p>
  <p>I've never used it but the idea is ...</p>
  <pre><code>mamba create -n mambaenv &lt;list of packages&gt;
  mamba activate mambaenv
  </code></pre>
  <p>The list of packages could be left blank for now, then,</p>
  <pre><code>mamba install &quot;Python&gt;=3.10.0&quot; numpy pandas pathlib
  mamba install longstitch 
  </code></pre>
  <p>Can also do</p>
  <pre><code>mamba install -n mambaenv longstitch
  </code></pre>
  <p><strong>NOTE</strong> longstitch exists strictly in -c bioconda. You do not seem to search and install via channels in mamba</p>
  <p>You search for a package and its dependencies via</p>
  <pre><code>mamba repoquery search longstitch
  mamba repoquery depends -a longstitch
  </code></pre>
  <p>It is important to place a virtual environment between the system Python and package Python (don't want a system corruption).</p>
  <hr />
  <p>Finally ...
  For <code>fa.fa</code> ... hmmmm, try <code>ls *.fa</code> and check for <code>.fa.fa</code> files.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-20T00:54:57.617Z
Answers.LastActivityDate: 2023-12-20T01:30:58.637Z
Answers.LastEditDate: 2023-12-20T01:30:58.637Z
Answers.UserDisplayName: M__
Body: <p>I installed <a href="https://github.com/bcgsc/LongStitch" rel="nofollow noreferrer">Longstitch</a> and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error.</p>
  <pre><code>(medaka) operations@LabPC1:~/medaka/longstitch-1.0.5$ ./longstitch run draft=~/medaka/~medaka/medaka_results/consensus.fa reads=~/medaka/combined.fastq G=4.5e8
  make: command: Command not found
  make: command: Command not found
  make: *** No rule to make target'/home/operations/medaka/~medaka/medaka_results/consensus.fa.fa', needed by'/home/operations/medaka/~medaka/medaka_results/consensus.fa.cut250.tigmint.fa'.  Stop.
  </code></pre>
  <p>I changed the file name from .fasta to .fa for my draft assembly because it requires a .fa file, but now I am getting &quot;.fa.fa&quot; What is wrong here?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-12-21T09:10:17.127Z
Comments.Text: Please provide a link and/or additional information about what Longstitch is. It would also be useful if you could provide a few lines of input and output (e.g. from both the example data and your own data).
Comments.UserDisplayName: gringer
Tags: <sequence-analysis><assembly><wgs><long-reads><scaffold>
Title: Longstitch error make: command: Command not found *** No rule to make target
ThreadText: # Longstitch error make: command: Command not found *** No rule to make target
  
  (Asked by: username_0 on 2023-12-19)
  
  I installed [Longstitch](https://github.com/bcgsc/LongStitch) and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error.
  
  ```
  (medaka) operations@LabPC1:~/medaka/longstitch-1.0.5$ ./longstitch run draft=~/medaka/~medaka/medaka_results/consensus.fa reads=~/medaka/combined.fastq G=4.5e8
  make: command: Command not found
  make: command: Command not found
  make: *** No rule to make target'/home/operations/medaka/~medaka/medaka_results/consensus.fa.fa', needed by'/home/operations/medaka/~medaka/medaka_results/consensus.fa.cut250.tigmint.fa'.  Stop.
  
  ```
  
  I changed the file name from .fasta to .fa for my draft assembly because it requires a .fa file, but now I am getting ".fa.fa" What is wrong here?
  
  **Tags:** sequence-analysis, assembly, wgs, long-reads, scaffold
  
  > **Comments:**
  > **username_1**: Please provide a link and/or additional information about what Longstitch is. It would also be useful if you could provide a few lines of input and output (e.g. from both the example data and your own data).  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2023-12-21. Score: 1
  
  The main issue I can see is the filenames, and should be easily solvable.
  
  Simply put, LongStitch is *very* particular about filenames. It expects the input draft to have the extension .fa, and the input reads to have any from a range of extensions (your .fastq is perfectly fine, though).
  
  The main issue is that LongStitch expects the extensions to be *missing* from the command. So if your draft is draft is called `consensus.fa` and your reads are `combined.fastq`, then the command would include something like `draft=consensus reads=combined`, not `draft=consensus.fa reads=combined.fastq`.
  
  (unsure if it accepts input from different directories, or whether you'll need to move your input to the same directory as well)
  
  More generally, when having issues with a particular tool which is available via github, I would encourage you to have a look at the 'Issues' or 'Help' section. What I normally do is to delete the 'is:issue is:open' terms in the search bar, which allows me to search for my bug among older, potentially solved issues (e.g. <https://github.com/bcgsc/LongStitch/issues/54>), and also generally to check that the software is still supported.
  
  Good luck!
  
  (\*that said, M\_'s suggestion of using mamba is generally a good one, and has helped me with another LongStitch bug)
  
  
  ---
  
  ### Answer by username_3 on 2023-12-20. Score: 1
  
  Could you download it from `conda` and try again? Its here, <https://docs.conda.io/en/main/miniconda.html>
  
  Then,
  
  ```
  conda create --name myenv
  conda activate myenv
  conda install -c bioconda longstitch
  longstitch ...
  
  ```
  
  Conda avoids all the build stuff.
  
  ---
  
  Notes
  
  If you find that "conda" is slow and doesn't ever load.
  
  There is an alternative to conda called **mamba**, this is fast and designed to address this exact issue. I have never needed to use it so the following is a rough guide only.
  
  Download and install via
  
  ```
  conda create --name myenv
  conda activate myenv
  conda install -c conda-forge mamba
  
  ```
  
  The documentation is here, <https://mamba.readthedocs.io/en/latest/user_guide/mamba.html>
  
  I've never used it but the idea is ...
  
  ```
  mamba create -n mambaenv <list of packages>
  mamba activate mambaenv
  
  ```
  
  The list of packages could be left blank for now, then,
  
  ```
  mamba install "Python>=3.10.0" numpy pandas pathlib
  mamba install longstitch 
  
  ```
  
  Can also do
  
  ```
  mamba install -n mambaenv longstitch
  
  ```
  
  **NOTE** longstitch exists strictly in -c bioconda. You do not seem to search and install via channels in mamba
  
  You search for a package and its dependencies via
  
  ```
  mamba repoquery search longstitch
  mamba repoquery depends -a longstitch
  
  ```
  
  It is important to place a virtual environment between the system Python and package Python (don't want a system corruption).
  
  ---
  
  Finally ...
  For `fa.fa` ... hmmmm, try `ls *.fa` and check for `.fa.fa` files.
  
  
  ---
  
  