Body: <p>I'm working on a project where I have to assemble sequences generated by RADseq. At the end I hope to compare two species of woodpeckers in Sri Lanka by using SNPs. </p>
  
  <p>I tried to assemble it using Stacks pipeline, but it crushed on the way with:</p>
  
  <blockquote>
  <pre><code>*** Error in `ustacks': malloc(): memory corruption: 0x000055db58024be0 ***
  </code></pre>
  </blockquote>
  
  <p>Are there are any other tools or pipelines that I can use for assembling my data instead?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-14T07:55:45.433Z
Comments.Text: There are plenty, see a list [here](https://omictools.com/rad-seq-category).
  
  If you want a better answer, write a specific question, write what you tried, why Stacks doesn't work and what is the desired output.
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-14T09:50:12.700Z
Comments.Text: @ShanikaLasanthi I tried to make your question clearer, it would be good to add the details about how you run stacks and what kind of error message you got before it crushed.
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-25T22:09:38.560Z
Comments.Text: I don't think you should be assembling RADseq, you should be aligning it.
Comments.UserDisplayName: Dan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-31T09:03:57.723Z
Comments.Text: I am getting this error saying "*** Error in `ustacks': malloc(): memory corruption: 0x000055db58024be0 ***"
  what am I supposed to do now?
Comments.UserDisplayName: Shanika Lasanthi
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-16T11:05:50.580Z
Comments.Text: @ShanikaLasanthi Which command did you use?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-18T03:05:12.497Z
Comments.Text: I used the code denovo_map.pl -s trim_ln7_brds_KD03S01.fastq -o ./stacks -b 1 -B trial1_radtags -t -T 15 -m 3 -M 2 -n 1.
Comments.UserDisplayName: Shanika Lasanthi
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-18T03:10:25.337Z
Comments.Text: I figured out what happened. My sequences were not in the same length,therefore it interfered with the algorithm giving this error. once I trimmed the sequences into the same length, pipeline was implemented successfully without giving any error. 
  Thank you all for the suggestions and the advice.
Comments.UserDisplayName: Shanika Lasanthi
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-20T09:22:31.230Z
Comments.Text: @ShanikaLasanthi it would be nice if you write here an actual answer for your question. It seems that the solution is not very intuitive and it could be very helpful for others to see the answer.
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-23T04:02:12.693Z
Comments.Text: Well, first my sequences were in different lengths between 50-100bp. I got the error when I used these sequences in the pipeline. When I checked the denovo log file for the run ( you can find it in the output folder you have mentioned for the run) there was a warning saying "different sequence lengths detected, this will interfere with Stacks algorithms."
  Therefore I trimmed the samples into 80bp and filtered out sequences shorter than 80bp.
  After that I did not get the error message and the pipeline was implemented successfully.
  And I hope this helps.
Comments.UserDisplayName: Shanika Lasanthi
Tags: <ngs><assembly><radseq>
Title: Assembling sequence data generated by RADseq
ThreadText: # Assembling sequence data generated by RADseq
  
  (Asked by: username_0 on 2017-06-14)
  
  I'm working on a project where I have to assemble sequences generated by RADseq. At the end I hope to compare two species of woodpeckers in Sri Lanka by using SNPs.
  
  I tried to assemble it using Stacks pipeline, but it crushed on the way with:
  
  > ```
  > *** Error in `ustacks': malloc(): memory corruption: 0x000055db58024be0 ***
  >
  > ```
  
  Are there are any other tools or pipelines that I can use for assembling my data instead?
  
  **Tags:** ngs, assembly, radseq
  
  > **Comments:**
  > **username_1**: There are plenty, see a list [here](https://omictools.com/rad-seq-category).  If you want a better answer, write a specific question, write what you tried, why Stacks doesn't work and what is the desired output.  
  > **username_1**: @username_0 I tried to make your question clearer, it would be good to add the details about how you run stacks and what kind of error message you got before it crushed.  
  > **username_2**: I don't think you should be assembling RADseq, you should be aligning it.  
  > **username_0**: I am getting this error saying "*** Error in `ustacks': malloc(): memory corruption: 0x000055db58024be0 ***" what am I supposed to do now?  
  > **username_3**: @username_0 Which command did you use?  
  > **username_0**: I used the code denovo_map.pl -s trim_ln7_brds_KD03S01.fastq -o ./stacks -b 1 -B trial1_radtags -t -T 15 -m 3 -M 2 -n 1.  
  > **username_0**: I figured out what happened. My sequences were not in the same length,therefore it interfered with the algorithm giving this error. once I trimmed the sequences into the same length, pipeline was implemented successfully without giving any error.  Thank you all for the suggestions and the advice.  
  > **username_1**: @username_0 it would be nice if you write here an actual answer for your question. It seems that the solution is not very intuitive and it could be very helpful for others to see the answer.  
  > **username_0**: Well, first my sequences were in different lengths between 50-100bp. I got the error when I used these sequences in the pipeline. When I checked the denovo log file for the run ( you can find it in the output folder you have mentioned for the run) there was a warning saying "different sequence lengths detected, this will interfere with Stacks algorithms." Therefore I trimmed the samples into 80bp and filtered out sequences shorter than 80bp. After that I did not get the error message and the pipeline was implemented successfully. And I hope this helps.  
  
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  ## 0 answers
  
  