<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>

CC BY-SA 3.0
2017-06-14T07:55:45.433Z
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.
Kamil S Jaron
CC BY-SA 3.0
2017-06-14T09:50:12.700Z
@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.
Kamil S Jaron
CC BY-SA 3.0
2017-06-25T22:09:38.560Z
I don't think you should be assembling RADseq, you should be aligning it.
Dan
CC BY-SA 3.0
2017-08-31T09:03:57.723Z
I am getting this error saying "*** Error in `ustacks': malloc(): memory corruption: 0x000055db58024be0 ***"
what am I supposed to do now?
Shanika Lasanthi
CC BY-SA 3.0
2017-11-16T11:05:50.580Z
@ShanikaLasanthi Which command did you use?
llrs
CC BY-SA 3.0
2017-11-18T03:05:12.497Z
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.
Shanika Lasanthi
CC BY-SA 3.0
2017-11-18T03:10:25.337Z
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.
Shanika Lasanthi
CC BY-SA 3.0
2017-11-20T09:22:31.230Z
@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.
Kamil S Jaron
CC BY-SA 3.0
2017-11-23T04:02:12.693Z
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.
Shanika Lasanthi
<ngs><assembly><radseq>
Assembling sequence data generated by RADseq
# 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**: @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.  
> **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**: @ShanikaLasanthi 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**: @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.  
> **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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