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Old 08-27-2015, 05:37 AM   #1
Coregonus
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Location: Munich

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Default Failed assembly due to memory limits in pyRAD

Hi all,

I am trying to do some population genetics using reduced genomic sequence data with little variation between samples. I am analyzing 500 RAD samples in pyRAD versions 3.0.6 (dereneaton.com/software/pyrad/). Finally, it completed step 6 (clustering of consensus sequences) but when running step 7 it just produces the .loci and the .excluded_loci files (both files look quite good). However, the pyRAD doesn’t generate any other output-files (and any error messages). D. Eaton (the developer of pyRAD) thinks that my dataset is too large and the program fails due to memory limits. What can I do?

Thanks in advance,
Alex
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