# Pre.cluster is taking forever

**URL:** <https://forum.mothur.org/t/pre-cluster-is-taking-forever/21340>\
**Category:** mothur bugs\
**Created:** [March 18, 2022, 4:17pm UTC](https://forum.mothur.org/t/pre-cluster-is-taking-forever/21340 "2022-03-18T16:17:16Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Alexandre\_Thibodeau](https://avatars.discourse-cdn.com/v4/letter/a/e480ec/32.png) [@Alexandre\_Thibodeau](https://forum.mothur.org/u/Alexandre_Thibodeau)\
**Post date:** [March 18, 2022, 4:17pm UTC](https://forum.mothur.org/t/pre-cluster-is-taking-forever/21340/1 "2022-03-18T16:17:16Z")

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Hello, me again with problems in 1.47.

For my precluster. using the new 1.47, preculster takes forever. For example i use to be able to do

| # of unique seqs: | 4620021 |
| --- | --- |
| total # of seqs: | 61662310 |

It took 9177 secs to run pre.cluster.

But with version 1.47: after 24 hours it is still not finished.

| # of unique seqs: | 4619994 |
| --- | --- |
| total # of seqs: | 61662283 |

…? untill finished.

Question: Is it because processors are not automatically set to my regular 32? I did set it to 32 at the beginning of the run though.

mothur \> set.logfile(name=megacampy\_logFile\_clustersplit)

Setting logfile name to megacampy\_logFile\_clustersplit

mothur \> set.current(processors=32)

Using 32 processors.

Current files saved by mothur:  
processors=32

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**Author:** ![Alexandre\_Thibodeau](https://avatars.discourse-cdn.com/v4/letter/a/e480ec/32.png) [@Alexandre\_Thibodeau](https://forum.mothur.org/u/Alexandre_Thibodeau)\
**Post date:** [March 21, 2022, 2:02pm UTC](https://forum.mothur.org/t/pre-cluster-is-taking-forever/21340/2 "2022-03-21T14:02:04Z")

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Turns out I was missing a count parameter in my first unique.seqs (forgot to update all the code to v1.47).  
That was generating a count without group info thus forcing mothur to only use 1 processor, which also caused trouble for my shared file.

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**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [March 31, 2022, 2:02pm UTC](https://forum.mothur.org/t/pre-cluster-is-taking-forever/21340/3 "2022-03-31T14:02:08Z")

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