# Trouble with \`alignment mafft\`

**URL:** https://forum.qiime2.org/t/trouble-with-alignment-mafft/22429
**Category:** Technical Support
**Created:** [March 10, 2022, 1:38pm UTC](https://forum.qiime2.org/t/trouble-with-alignment-mafft/22429 "2022-03-10T13:38:05Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![Nana\_Amoako](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nana_amoako/32/13001_2.png) [@Nana\_Amoako](https://forum.qiime2.org/u/Nana_Amoako)
#### Post date: [March 10, 2022, 1:38pm UTC](https://forum.qiime2.org/t/trouble-with-alignment-mafft/22429/1 "2022-03-10T13:38:05Z")

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![Thurs, 10 March](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/0/0817cf292e400b9d032073e17a4108e1b029ff7a.png)

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.

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### Author: ![Keegan-Evans](https://forum.qiime2.org/user_avatar/forum.qiime2.org/keegan-evans/32/10422_2.png) [@Keegan-Evans](https://forum.qiime2.org/u/Keegan-Evans)
#### Post date: [March 10, 2022, 1:42pm UTC](https://forum.qiime2.org/t/trouble-with-alignment-mafft/22429/2 "2022-03-10T13:42:21Z")

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### Author: ![Keegan-Evans](https://forum.qiime2.org/user_avatar/forum.qiime2.org/keegan-evans/32/10422_2.png) [@Keegan-Evans](https://forum.qiime2.org/u/Keegan-Evans)
#### Post date: [March 15, 2022, 4:43pm UTC](https://forum.qiime2.org/t/trouble-with-alignment-mafft/22429/3 "2022-03-15T16:43:48Z")

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@Nana_Amoako,

From what you have posted here it looks like you are running out of memory:  
 ![mafft_mem_issue](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/optimized/2X/a/a5657e7eb0631d35ffea7457663af70d2b4a17eb_2_690x46.jpeg)

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](https://forum.qiime2.org/t/q2-alignment-reference-based-alignment-using-sina/6220)!

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### Author: ![Keegan-Evans](https://forum.qiime2.org/user_avatar/forum.qiime2.org/keegan-evans/32/10422_2.png) [@Keegan-Evans](https://forum.qiime2.org/u/Keegan-Evans)
#### Post date: [March 15, 2022, 4:44pm UTC](https://forum.qiime2.org/t/trouble-with-alignment-mafft/22429/4 "2022-03-15T16:44:18Z")

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 15, 2022, 10:44pm UTC](https://forum.qiime2.org/t/trouble-with-alignment-mafft/22429/5 "2022-04-15T22:44:29Z")

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