I figured out the vsearch part of it but now i face this issue when running mafft for alignment.
I need help with this. Thank you.
From what you have posted here it looks like you are running out of memory:
How big is your dataset? I am not sure about precise cuttoffs(this is not a tool that I have used a lot), but mafft does not handle large datasets well as the memory requirements increase quickly with increasing dataset size.
You can try increasing the amount of available memory, however, with a large enough dataset a sufficient amount may be difficult/impossible to achieve. Normally, I would suggest reducing the number of threads you are using, however you are already only using one, but I want to note this for future readers.
I think your best bet is to use a reference based SINA alignment, check out @epruesse's community tutorial on how to do this here!
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